PDB-5b8c: High resolution structure of the human PD-1 in complex with pembr...

ID or keywords:

Entry

Database: PDB / ID: 5b8c

Title

High resolution structure of the human PD-1 in complex with pembrolizumab Fv

Components

Pembrolizumab heavy chain variable region (PemVH)
Pembrolizumab light chain variable region (PemVL)
Programmed cell death protein 1

Keywords

IMMUNE SYSTEM / antibody

Function / homology

Function and homology information

negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.146 Å

Authors

Horita, S. / Shimamura, T. / Iwata, S. / Nomura, N.

Funding support

Japan, 4items

Organization	Grant number	Country
Japan Science and Technology Agency (JST)		Japan
Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan		Japan
Japan Society for the Promotion of Science	15K06968	Japan
Japan Society for the Promotion of Science	15J04343	Japan

Citation

Journal: Sci Rep / Year: 2016
Title: High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1
Authors: Horita, S. / Nomura, Y. / Sato, Y. / Shimamura, T. / Iwata, S. / Nomura, N.

History

Deposition	Jun 14, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Derived calculations Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Oct 18, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5b8c.cif.gz	549.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5b8c.ent.gz	454.6 KB	Display	PDB format
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Validation report

Summary document	5b8c_validation.pdf.gz	501.7 KB	Display	wwPDB validaton report
Full document	5b8c_full_validation.pdf.gz	513.2 KB	Display
Data in XML	5b8c_validation.xml.gz	48.6 KB	Display
Data in CIF	5b8c_validation.cif.gz	68.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/5b8c ftp://data.pdbj.org/pub/pdb/validation_reports/b8/5b8c	HTTPS FTP

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Related structure data

Related structure data	3rrqS 5dk3S S: Starting model for refinement
Similar structure data	4n1e-1 1dzb-2 1dzb-1 5x9b-d 5eqf-2 3tti-d 5jw7-d 5eqf-3 1oaz-1 4n1e-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3rrqS

5dk3S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#204 - Dec 2016 PD-1 similarity (3) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#204 - Dec 2016
PD-1
similarity (3)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)

Deposited unit

A: Pembrolizumab light chain variable region (PemVL)

B: Pembrolizumab heavy chain variable region (PemVH)

C: Programmed cell death protein 1

D: Pembrolizumab light chain variable region (PemVL)

E: Pembrolizumab heavy chain variable region (PemVH)

F: Programmed cell death protein 1

G: Pembrolizumab light chain variable region (PemVL)

H: Pembrolizumab heavy chain variable region (PemVH)

I: Programmed cell death protein 1

J: Pembrolizumab light chain variable region (PemVL)

K: Pembrolizumab heavy chain variable region (PemVH)

L: Programmed cell death protein 1

168 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pembrolizumab light chain variable region (PemVL)

B: Pembrolizumab heavy chain variable region (PemVH)

C: Programmed cell death protein 1

defined by author&software
42 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Pembrolizumab light chain variable region (PemVL)

E: Pembrolizumab heavy chain variable region (PemVH)

F: Programmed cell death protein 1

defined by author&software
42 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Pembrolizumab light chain variable region (PemVL)

H: Pembrolizumab heavy chain variable region (PemVH)

I: Programmed cell death protein 1

defined by author&software
42 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Pembrolizumab light chain variable region (PemVL)

K: Pembrolizumab heavy chain variable region (PemVH)

L: Programmed cell death protein 1

defined by author&software
42 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.680, 143.130, 76.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Pembrolizumab light chain variable region (PemVL) Mass: 12991.460 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Brevibacillus choshinensis (bacteria)
#2: Antibody	Pembrolizumab heavy chain variable region (PemVH) Mass: 13494.995 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Brevibacillus choshinensis (bacteria)
#3: Protein	Programmed cell death protein 1 / hPD-1 Mass: 15514.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Brevibacillus choshinensis (bacteria) / References: UniProt: Q15116
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 0.2 M KNO3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.146→45.418 Å / Num. obs: 86668 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.094 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.15→2.2 Å

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2210: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RRQ, 5DK3

3rrq

5dk3

Resolution: 2.146→45.418 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.18

	R_factor	Num. reflection	% reflection
R_free	0.2259	4460	5.15 %
R_work	0.1839	-	-
obs	0.186	86668	99.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.146→45.418 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10591	0	0	271	10862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10860
X-RAY DIFFRACTION	f_angle_d	0.73	14763
X-RAY DIFFRACTION	f_dihedral_angle_d	16.049	6401
X-RAY DIFFRACTION	f_chiral_restr	0.048	1608
X-RAY DIFFRACTION	f_plane_restr	0.005	1906

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1464-2.1834	0.3448	220	0.3073	4011	X-RAY DIFFRACTION	93
2.1834-2.2231	0.3126	238	0.2908	4001	X-RAY DIFFRACTION	94
2.2231-2.2659	0.3418	233	0.2843	4066	X-RAY DIFFRACTION	94
2.2659-2.3122	0.3338	213	0.2845	4098	X-RAY DIFFRACTION	95
2.3122-2.3624	0.3173	236	0.2777	4019	X-RAY DIFFRACTION	94
2.3624-2.4174	0.3497	250	0.2766	4070	X-RAY DIFFRACTION	94
2.4174-2.4778	0.3267	226	0.2773	4060	X-RAY DIFFRACTION	95
2.4778-2.5448	0.3345	213	0.2659	4094	X-RAY DIFFRACTION	95
2.5448-2.6197	0.3262	226	0.2496	4085	X-RAY DIFFRACTION	95
2.6197-2.7042	0.3063	189	0.2342	4137	X-RAY DIFFRACTION	96
2.7042-2.8009	0.2293	202	0.212	4098	X-RAY DIFFRACTION	95
2.8009-2.913	0.2283	198	0.2024	4112	X-RAY DIFFRACTION	95
2.913-3.0456	0.2452	188	0.2015	4141	X-RAY DIFFRACTION	95
3.0456-3.2061	0.2527	200	0.1881	4115	X-RAY DIFFRACTION	95
3.2061-3.4069	0.2174	236	0.1827	4119	X-RAY DIFFRACTION	94
3.4069-3.6698	0.1975	231	0.1669	4138	X-RAY DIFFRACTION	95
3.6698-4.0389	0.1904	243	0.1496	4114	X-RAY DIFFRACTION	94
4.0389-4.6229	0.1876	230	0.126	4165	X-RAY DIFFRACTION	95
4.6229-5.8224	0.1507	230	0.1288	4209	X-RAY DIFFRACTION	94
5.8224-45.4283	0.1926	236	0.1674	4368	X-RAY DIFFRACTION	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.2951	-6.7483	7.372	5.1551	-5.9431	7.222	-0.66	-0.6868	-0.1049	1.2958	0.6894	-0.2356	-1.3345	-0.8618	0.004	0.5869	-0.04	0.0545	0.4718	-0.0446	0.2379	-11.4785	10.1188	30.4137
2	4.0363	-0.3762	-1.4978	4.7121	-0.0932	0.5832	-0.2669	0.3867	0.6157	-0.0671	0.2382	0.286	-0.6558	-0.0217	-0.016	0.4717	-0.0443	0.064	0.5206	0.0846	0.2613	-14.6513	15.461	15.6728
3	1.3286	-0.5966	-0.7958	1.5242	-0.0881	1.6173	-0.1767	0.1522	0.0739	-0.0085	0.1416	-0.4279	-0.279	-0.0059	-0.0469	0.4604	-0.0403	0.096	0.5717	-0.0068	-0.0228	-10.988	1.992	22.2524
4	3.071	-0.5659	0.8588	1.442	0.2659	0.9379	0.2129	0.2626	0.4208	-0.3072	-0.2079	-0.1571	0.2339	0.0657	-0.0313	0.4891	-0.0536	0.0825	0.4719	0.009	0.1939	-7.1692	4.4008	15.6165
5	5.8145	-0.8414	0.8848	5.5933	0.862	0.4685	0.2491	0.1889	0.4553	-0.4177	-0.0012	0.2116	-0.1464	-0.2582	-0.1377	0.3951	-0.0827	0.0498	0.4941	0.0324	0.2	-17.3139	7.5034	15.2275
6	0.4696	-0.0376	0.273	1.818	-0.5882	3.648	0.0504	-0.0577	-0.0061	0.4651	0.0207	-0.1321	-0.3943	0.3886	0.0229	0.4528	-0.0492	0.03	0.6635	0.0256	0.0787	-10.7948	1.7455	31.7278
7	2.0065	-7.6585	6.9604	6.9436	-5.8717	5.104	-0.3277	0.2503	0.0902	-0.1765	0.5276	0.7087	-0.8007	-0.1691	-0.227	0.5667	-0.0441	-0.0383	0.605	0.0752	0.3569	-22.9291	15.4438	14.35
8	1.9444	0.4556	1.3518	3.0766	-0.7915	2.3269	0.1072	0.3289	-0.1549	-0.0927	-0.0945	0.464	-0.1098	-0.8346	-0.1327	0.433	-0.0272	0.0131	0.5224	0.094	0.1577	-30.8175	-10.6049	28.3972
9	6.913	-1.8585	-6.5594	1.4756	3.2165	8.409	0.2844	0.5906	0.1002	-0.146	-0.133	-0.031	-0.0195	-0.6922	-0.0385	0.472	0.0412	0.009	0.5333	0.0557	0.157	-22.9828	-16.5163	24.6707
10	0.1642	0.057	0.1971	0.2066	-0.2814	0.8041	-0.1699	0.147	-0.0904	0.057	0.0721	0.0458	0.0407	0.1198	-0.051	0.419	-0.0703	0.068	0.7194	-0.0417	-0.0387	-16.6853	-11.0698	27.3244
11	0.3079	-0.1735	0.0797	0.7947	-0.2679	1.49	-0.1054	-0.4911	0.4486	0.5241	0.3114	0.3881	-0.0891	-0.2508	0.1229	0.4933	0.0875	0.0557	0.7458	-0.0167	-0.4107	-17.5882	-6.5481	34.8541
12	2.1044	-1.0495	-0.4158	3.9169	1.0374	1.66	0.0486	-0.4857	-0.0618	0.6742	-0.08	-0.1702	0.022	0.1683	0.0507	0.5652	0.0079	0.0441	0.6896	0.0362	0.1491	-21.5259	-13.9585	37.9834
13	2.5584	-1.6481	-0.3642	8.2907	5.7755	4.536	0.0327	-0.3256	-0.2998	0.5358	0.0554	0.2173	0.023	-0.3545	-0.1157	0.4142	-0.0109	0.0112	0.4712	0.0601	0.1879	-23.7731	-18.1141	30.504
14	4.1043	2.2942	-0.4572	5.613	-5.1736	5.7839	-0.901	-1.0375	-0.075	1.3087	0.4842	-0.08	-0.3925	-1.0776	0.403	0.5698	0.098	0.091	0.641	0.016	0.2704	-31.3966	-2.3761	40.5925
15	0.7334	-0.1703	0.2403	0.4576	-0.36	0.2982	0.0812	0.0857	-0.0218	0.0181	-0.0102	0.1134	0.0811	-0.0195	-0.0697	0.4362	-0.0129	0.055	0.5067	0.0381	0.1434	-19.631	-7.4434	25.9111
16	1.7427	-0.7726	-1.0372	1.1195	0.3532	1.9117	0.061	0.4925	0.2977	-0.2132	-0.0337	-0.1798	-0.1034	0.0593	-0.0567	0.3926	-0.0312	0.0501	0.4841	-0.0078	0.1713	-12.9546	-8.7075	22.0708
17	1.8693	2.3775	3.5999	3.4643	4.5066	6.9353	0.5044	-0.4827	-0.0348	-0.5118	-0.5509	0.8921	-0.3011	-1.1169	0.0465	0.4641	0.0441	0.0275	0.6709	0.0145	0.2539	-35.7814	-3.3178	33.6052
18	2.3603	-2.0871	-0.5408	2.656	-1.5903	8.5572	0.0513	-0.4857	0.1547	0.4993	-0.1071	-0.3608	0.0199	1.0688	-0.0422	0.3542	-0.0557	-0.1211	0.5758	-0.0713	0.3298	11.0011	-22.9906	29.6539
19	1.9676	-2.1337	3.079	6.8274	-7.616	8.8289	-0.1019	-0.2582	0.2245	0.9536	0.2216	-0.1692	-1.186	0.1923	-0.1612	0.4357	-0.0336	0.0279	0.5573	-0.0764	0.2386	10.7991	-13.4321	24.7985
20	0.8953	-0.1342	-0.2088	5.3516	0.7744	0.1368	0.3115	-0.018	0.1463	0.443	-0.2093	0.1339	0.0159	0.324	-0.0825	0.3848	0.0024	-0.0364	0.5116	-0.0227	0.1872	2.4716	-17.5179	26.3382
21	2.7123	2.8408	-2.1893	6.8169	-3.799	4.9442	-0.4243	-0.0143	0.0425	-0.3662	0.8214	0.2534	0.2524	-0.2009	-0.3702	0.4351	0.0727	0.027	0.5542	0.0011	0.1921	-2.6663	-21.3667	27.8867
22	3.0365	-1.3831	-1.4511	0.9043	-0.3077	3.6334	-0.0235	-0.9515	0.5378	0.1442	0.2264	-0.2273	-0.0383	0.0843	-0.1811	0.4212	0.0119	-0.04	0.5014	-0.0591	0.2381	5.7475	-12.4832	33.2315
23	1.598	-1.5274	-2.4174	1.4626	2.3063	3.6603	-0.3104	-0.6528	-0.0443	2.0811	-0.3982	0.2853	1.2489	-0.3975	0.7552	0.8191	-0.066	-0.0407	0.7186	-0.0293	0.3318	3.1481	-25.7561	42.3027
24	0.9413	-1.6586	-0.4165	9.1609	0.3064	0.2011	0.1937	0.1856	-0.0043	-0.436	-0.031	-0.1799	0.1264	-0.0792	-0.2625	0.3864	-0.0304	0.0089	0.5656	-0.0318	0.1798	2.6272	-17.8193	20.0052
25	4.9305	2.8699	1.6047	4.7168	0.5029	1.4719	-0.3044	-0.6906	-0.1149	1.5888	-0.0404	-0.3747	0.2937	-0.1233	0.3269	0.7577	0.1888	-0.0384	0.5419	-0.0058	0.3763	7.9229	-31.6594	37.2191
26	1.6793	-0.7069	1.9418	6.5854	2.654	4.1466	0.38	0.6125	-0.0437	-0.5162	-0.064	0.0735	-0.2806	-0.5258	-0.2738	0.4083	0.0007	-0.0561	0.6474	0.0191	0.178	-46.2035	-23.828	-11.5592
27	3.0839	0.1972	3.3233	5.1259	-1.6759	4.2434	0.0315	-0.3701	0.2063	0.1651	0.2353	0.2105	0.3701	-0.8717	-0.1984	0.3928	-0.0306	0.0467	0.6003	0.0402	0.3835	-53.2838	-17.5345	6.9243
28	5.9996	-3.8696	-4.9436	5.5392	1.5163	5.3241	0.0367	-0.823	-0.6416	-0.0006	-0.4798	0.0987	-0.5354	0.6233	0.4148	0.3158	-0.0578	-0.0591	0.5335	0.0395	0.3025	-48.9374	-25.292	-2.3603
29	5.7865	1.1463	-0.9143	8.5807	-2.2537	5.5146	0.0301	0.6424	-0.0491	-0.9713	-0.4939	0.0224	0.579	0.1966	0.382	0.325	0.0279	-0.0192	0.4685	0.0136	0.2363	-38.246	-34.9232	-9.3576
30	2.3266	-0.9507	-1.4398	4.9896	-1.0654	1.5127	0.0388	-0.4051	0.1761	0.3387	0.1229	-0.3175	0.1465	-0.1875	-0.0855	0.3456	-0.0217	0.0192	0.5717	0.0365	0.1284	-37.9267	-17.3336	0.2892
31	2.3422	-1.0427	-3.0363	3.1989	2.8629	4.7567	-0.0656	-0.4486	-0.172	0.1771	0.2113	-0.0157	-0.1716	-0.0471	-0.1323	0.3529	0.0071	-0.0279	0.611	0.0775	0.212	-35.679	-26.5078	6.0823
32	4.8227	-2.8171	-3.969	6.5625	7.3151	9.6743	-0.246	-0.1342	-0.1405	0.1005	0.1307	0.6448	-0.0769	-0.166	-0.0022	0.3412	-0.0444	0.0102	0.4706	0.0704	0.2012	-45.0903	-28.8258	0.7506
33	1.3258	-1.3407	0.0255	2.9376	0.3706	1.1649	0.0489	-0.3869	-0.2365	0.2359	0.1358	0.4352	-0.2001	0.1581	-0.1267	0.4522	-0.0324	0.0646	0.6577	0.0775	0.1752	-43.8972	-17.7355	3.6734
34	0.3697	0.4435	-0.5818	1.0536	-0.403	1.0948	0.3875	0.6494	-0.1471	-0.8965	-0.5472	0.0491	-0.0558	-0.1454	0.0864	0.4937	0.01	0.0112	0.6072	0.0045	0.194	-37.8004	-24.209	-12.654
35	7.1229	-3.5202	-5.5825	6.9225	4.4258	7.7789	1.0756	0.3605	-0.0833	0.2392	-0.9228	0.463	-0.8238	-1.6007	-0.069	0.5225	0.0273	0.0547	0.7712	0.0378	0.2344	-52.1058	-12.4463	4.3945
36	5.127	-0.1666	-0.7045	5.8066	2.529	1.189	0.2646	0.0607	0.4813	0.3992	-0.1202	-0.2352	-0.7574	0.7518	-0.1706	0.3155	-0.073	0.0785	0.5762	0.0146	0.2626	-26.276	-3.5368	-9.9819
37	2.4391	1.7747	-1.7347	9.7743	2.9273	3.3881	0.1946	-0.4076	-0.0922	0.4933	-0.0572	-0.9013	0.1684	0.1694	-0.0864	0.3469	-0.011	0.0141	0.6316	0.0709	0.3156	-20.3892	-10.4203	-7.2586
38	0.6668	0.5446	-1.2232	1.4352	0.3958	4.3808	0.2111	-0.4192	0.1787	0.2467	-0.0454	-0.3874	-0.2716	0.4961	0.0524	0.44	-0.0655	0.0135	0.7175	0.0169	-0.0341	-25.6261	-17.5005	-8.4621
39	5.3017	2.418	-2.9872	4.5711	2.7766	6.6216	-0.1513	1.3633	0.543	-0.7971	-0.3852	0.5725	-0.1711	-0.5674	0.3904	0.4827	0.044	-0.033	0.5166	0.0842	0.209	-35.669	-13.7908	-13.5778
40	0.2551	0.8252	0.6497	3.1684	0.4587	6.6774	0.4918	1.0467	0.4015	-0.5111	-0.4404	-0.5138	0.3806	0.6951	0.0937	0.5423	0.1119	0.1609	0.7277	0.0868	0.1927	-20.6032	-21.632	-15.8388
41	0.7086	1.7494	-1.3554	4.6937	-3.2833	2.5915	-0.3244	0.2099	0.0916	-2.015	0.3165	0.0148	0.4504	0.0454	-0.0074	0.6829	0.0522	-0.0401	0.7367	0.0756	0.2439	-32.4383	-14.4062	-22.9018
42	1.2252	-0.599	-0.2969	1.7244	0.3328	0.2862	0.1783	0.12	0.0165	-0.1608	-0.0989	-0.1257	-0.1125	0.0318	-0.0721	0.4291	0.0061	0.0301	0.6418	0.0515	0.1256	-27.2143	-12.1657	-11.0765
43	2.8382	-0.5836	-0.6526	2.4258	-0.2154	0.2331	-0.0307	-0.0157	-0.1945	-0.2402	0.0413	-0.1787	0.7111	0.3961	-0.0919	0.4816	0.0565	-0.0981	0.5387	-0.0562	0.2719	-12.7455	-45.5473	-9.5152
44	1.0648	-0.5078	-2.0419	1.672	-0.5117	8.1068	-0.1209	0.5102	-0.3076	0.0743	-0.0243	0.079	0.1309	-0.1965	0.0292	0.3421	0.026	-0.0708	0.5459	0.0137	0.1654	-20.7416	-41.2551	-5.6881
45	1.2967	-1.0971	-0.1157	3.9213	-0.2164	1.1436	0.1565	0.4317	-0.2102	-0.5532	0.0353	0.1759	-0.034	0.0363	-0.1984	0.3347	0.0268	-0.0496	0.4792	-0.0172	0.2432	-20.5976	-37.9912	-12.2055
46	1.8259	1.0796	-1.1295	7.538	-0.5761	0.6984	-0.3715	1.222	-0.1091	-0.8525	0.0582	-0.2527	-0.6002	1.5481	0.2446	0.5665	-0.0455	0.0602	1.0163	0.0072	0.2685	-8.9239	-37.8705	-22.5907
47	6.1429	-1.5567	-3.1201	0.9012	0.0589	2.6292	0.2456	-0.3678	-0.0536	0.0564	-0.0482	-0.0617	-0.2584	0.05	-0.1793	0.4247	-0.014	-0.0824	0.5581	0.005	0.1834	-17.689	-37.1462	-0.8141
48	5.6586	3.741	2.8351	2.922	1.3516	2.0267	-0.298	1.4207	-0.09	-0.5878	-0.1465	-0.3319	0.5369	1.773	0.4348	0.4778	0.1871	0.0563	0.8311	0.0447	0.4191	-4.026	-42.2525	-16.4077
49	7.3928	4.2061	5.7708	6.1125	4.6649	5.0331	0.6956	-0.7296	-0.49	1.0927	-0.3021	-0.3626	0.1105	0.1274	-0.3679	0.6209	0.0403	-0.0461	0.5792	0.0349	0.1782	-3.1508	-54.5753	36.5484
50	1.1238	1.4541	-1.021	9.6071	-0.677	1.0299	0.0792	-0.7944	-0.2129	0.4987	-0.066	-1.556	-0.1678	0.4321	-0.0445	0.3885	0.094	-0.1546	0.5618	-0.0361	0.56	13.5415	-44.6148	32.323
51	4.179	4.5494	-1.4735	5.0268	-1.4767	0.6875	-0.108	-0.3951	-0.4555	-0.092	0.0096	0.0696	0.1163	-0.0538	0.2787	0.4273	0.15	0.0108	0.464	0.0045	0.3517	-4.1969	-58.7174	26.8329
52	1.2142	-0.1053	0.5314	1.704	-1.1756	1.1289	-0.0848	0.2923	0.0208	-0.0094	-0.0668	-0.2185	-0.09	0.0312	0.1607	0.371	0.0393	0.0278	0.4721	-0.02	0.1965	-2.9315	-42.3818	26.9722
53	3.1661	2.0554	-0.1518	1.4187	-0.5562	4.3743	0.2378	0.5872	-0.0146	-0.0677	-0.0273	-0.1146	-0.1344	0.2158	-0.191	0.4137	0.0918	0.0697	0.5368	-0.0127	0.2912	-0.2556	-47.1022	17.7355
54	6.2054	7.6522	-1.7681	9.575	-2.175	0.4931	0.2347	-0.0235	0.0489	0.2615	-0.195	0.0821	0.0074	0.0788	-0.0233	0.4567	0.1179	0.0504	0.5548	-0.0135	0.2167	2.8723	-54.4899	25.5129
55	1.7914	1.0023	1.8383	2.3471	1.9845	2.3814	0.0975	-0.3766	0.0665	-0.0898	-0.1199	-0.0368	-0.1164	0.1757	0.0572	0.4045	0.1076	0.0084	0.4646	0.0279	0.2236	3.5669	-43.3133	28.7054
56	4.6855	-1.1263	1.4599	2.7525	-0.1819	0.463	-0.2917	0.2298	-0.5814	0.4474	0.1625	0.3921	0.272	0.405	0.084	0.5295	0.0188	0.0743	0.5224	0.01	0.2126	-10.7681	-52.9766	31.5217
57	4.6704	5.5065	3.593	6.9829	4.4307	2.843	0.6362	-1.2612	-0.1968	0.0426	-0.5085	-0.9042	-0.8097	-0.5821	-0.1574	0.5875	-0.044	0.0243	0.6359	0.0473	0.3303	10.2055	-40.7179	36.9829
58	2.7509	0.001	2.1445	4.1727	0.9002	1.8765	0.1439	-0.1053	0.1406	-0.06	-0.0233	0.1139	-0.2473	-0.2065	-0.0732	0.3571	0.0932	-0.0278	0.4671	0.0385	0.1977	-19.6306	-31.3803	33.1643
59	0.5417	0.4346	0.6791	3.8327	3.5424	3.595	-0.1025	0.0198	-0.034	-0.2077	-0.0579	0.1676	-0.0292	0.1393	0.1884	0.3475	0.0391	0.0148	0.4851	0.024	0.2037	-19.6007	-38.848	24.0579
60	5.5161	0.7187	0.2326	0.9662	-0.1097	0.0119	0.1209	-0.7395	0.5294	0.1417	-0.2214	-0.2858	0.2938	-0.0206	0.0154	0.482	0.0791	0.0126	0.6707	-0.0256	0.2298	-14.4307	-44.1089	35.5931
61	4.9363	-5.2781	2.8712	5.644	-3.1891	7.0905	0.8626	0.9557	-0.6348	-1.7366	-0.7906	1.8358	-0.5659	-0.1116	-0.1051	0.525	0.0232	-0.1132	0.5475	-0.0714	0.4086	-27.7352	-45.457	19.8576
62	8.5552	2.4866	4.7407	2.5417	0.961	2.724	0.3635	-0.7441	0.2229	1.0955	-0.2143	0.3001	0.329	-0.8712	-0.126	0.6111	-0.0454	0.079	0.512	0.042	0.2641	-23.1931	-49.0999	34.6332
63	9.3031	-0.6227	6.1149	1.5169	1.5545	6.6246	0.1518	-0.5535	-0.0768	0.0014	0.1004	0.1583	0.7788	-1.2263	-0.2785	0.3386	-0.0473	0.0546	0.428	-0.0242	0.4334	-28.211	-41.96	32.373
64	8.2139	-5.2584	5.354	8.3295	-7.5135	8.6451	-0.1446	-0.1659	0.2059	-0.3402	-0.1109	-0.1421	0.4167	-0.8283	0.1732	0.3847	-0.051	0.0068	0.3813	-0.0136	0.2197	-26.3405	-35.3431	26.5381
65	0.3413	0.0934	-0.0612	0.8181	-0.2568	1.1067	0.1141	-0.1302	-0.0557	0.1918	0.0704	0.2089	0.2784	0.0275	-0.0656	0.4759	0.0916	0.0187	0.7748	-0.0048	-0.081	-17.8461	-39.9091	35.0966
66	1.3461	0.0427	-0.3134	3.9445	3.0112	3.681	-0.1071	-0.1671	-0.0592	0.1212	0.3333	-0.1369	0.0082	0.6564	-0.1939	0.3853	0.0532	-0.0294	0.5089	0.0675	0.1776	-14.5078	-40.4582	27.1802
67	6.6149	2.4501	-4.2296	6.1665	-1.3682	8.4605	-0.1166	0.2159	-1.538	-0.572	-0.0574	-0.0694	1.1441	-0.1793	0.1115	0.7324	-0.0148	-0.186	0.5128	0.0266	0.3687	-27.3887	-62.8084	3.9623
68	8.9118	-0.4497	6.2997	6.7748	-4.7643	7.7526	0.0794	-0.1641	-0.267	-0.1363	0.409	0.0878	0.5075	-0.1677	-0.4561	0.4524	-0.0399	-0.0165	0.4523	-0.0424	0.2484	-23.0174	-56.2949	8.8461
69	5.7278	-2.0604	1.3664	7.861	1.9376	2.1446	0.2503	-0.2238	-0.7818	0.3021	0.0362	0.243	0.4848	-0.0693	-0.2834	0.5221	-0.0282	-0.0732	0.4601	0.0644	0.436	-22.2895	-62.6428	14.9711
70	7.0132	-0.0153	-2.8085	5.9096	-4.2777	6.6345	-0.1908	0.3643	-0.1019	-0.0287	0.2374	-0.1238	-0.0017	-0.5128	-0.0681	0.4254	0.0195	-0.1114	0.3758	-0.0393	0.2417	-27.1345	-56.6387	7.8247
71	3.0104	2.0162	1.9183	7.486	4.6073	9.6705	-0.1357	0.5799	-0.0558	-0.7374	0.9154	-0.8584	-0.0199	-0.1397	-0.7065	0.4042	-0.0795	0.1676	0.5723	-0.0372	0.4681	19.467	-32.1439	-16.8574
72	8.8854	2.0601	1.748	6.0362	0.7578	2.8201	-0.082	1.0099	-2.5641	-0.3773	0.1997	-0.454	0.0814	-0.1392	-0.1393	0.4518	0.0902	0.1943	0.5635	-0.158	0.9904	12.703	-45.2444	-12.2937
73	5.317	-4.7616	-5.2733	5.6632	4.6695	5.2772	0.2275	-0.7154	0.2207	0.1941	0.3946	-0.7906	-0.54	1.2108	-0.6731	0.3741	-0.0133	-0.0245	0.5825	-0.0249	0.5657	26.2958	-27.9213	-4.7627
74	1.1198	0.49	2.885	2.6247	-0.0473	8.0253	-0.0558	-0.3832	-0.138	0.0886	0.1298	0.0747	-0.0207	-0.5952	-0.0644	0.3092	0.0779	0.0732	0.4694	0.0736	0.4165	9.2195	-33.6191	-3.279
75	0.7709	1.4014	0.7745	5.9646	-0.3987	1.7397	0.146	0.0118	-0.2066	-0.1299	-0.0711	-0.4344	0.1113	0.0876	-0.0759	0.2707	0.0843	0.0545	0.4363	0.0613	0.3505	12.6283	-38.9187	-7.6093
76	7.3278	8.0031	3.2429	2.0599	2.8558	4.0488	-0.3376	0.2974	-1.2761	-0.1681	0.5069	-1.1125	-0.0456	-0.0347	-0.229	0.4465	0.0645	-0.0074	0.5563	-0.0791	0.5936	13.8829	-32.0711	-13.5735
77	6.0945	-2.0016	3.1002	5.2246	0.3893	2.0167	0.106	0.1781	-0.1818	-0.2923	0.2666	0.4198	0.4143	-0.5516	-0.3288	0.2905	0.0937	0.0399	0.3946	-0.0263	0.2957	-2.9846	-15.3028	-13.6153
78	2.0547	0.4144	1.3554	1.0589	0.5616	0.9642	-0.0138	-0.2501	0.0346	-0.0418	-0.082	0.0702	-0.2439	-0.2994	0.1368	0.4706	0.0948	0.0689	0.5667	0.0373	0.215	4.5431	-15.595	-4.3493
79	7.2958	4.118	2.8607	6.6889	5.7375	5.3741	-0.3774	0.3045	0.0049	-0.4476	0.4137	0.0386	-0.235	0.5404	-0.0761	0.5347	0.043	0.086	0.4653	0.0654	0.1908	10.9668	-15.8228	-10.8273
80	6.2872	-5.9685	3.2497	8.9766	0.3667	5.3001	-0.2056	0.6407	1.2887	-1.155	0.5256	-1.1676	0.6901	0.2386	-0.4641	0.5669	-0.1107	0.1984	0.6985	-0.0211	0.4587	13.8423	-11.51	-19.409
81	2.296	0.177	1.8622	0.7702	0.3424	5.2585	-0.0195	0.1605	-0.0516	-0.2688	0.0444	-0.0494	-0.2797	-0.1211	-0.0108	0.4192	0.05	0.0702	0.4856	0.0251	0.1981	4.9152	-15.9437	-10.2836
82	4.7088	0.7086	1.7953	5.3324	1.7189	6.5657	0.0426	-0.1268	0.2039	0.0026	0.5892	-0.8155	-0.2594	0.3106	-0.5509	0.3393	-0.0086	0.1314	0.5153	-0.0908	0.4702	24.576	-11.5424	12.8407
83	6.5783	-0.0696	1.237	4.4164	-0.0007	0.4892	0.076	0.9693	-0.2006	-0.2174	0.0608	-0.9813	-0.316	0.4028	-0.1401	0.4558	0.0124	0.1502	0.6432	-0.059	0.5778	27.2696	-14.5071	2.5085
84	4.6287	2.781	-1.7082	4.5877	1.1293	7.9793	0.2472	0.2183	0.5162	-0.5912	0.4317	-1.027	-1.2888	0.1107	-0.568	0.584	-0.0965	0.1728	0.5755	-0.0562	0.6855	29.4251	-4.6169	7.2764
85	3.8425	-4.3899	-0.4113	5.6609	-1.6197	6.6289	0.4451	0.1701	-0.7442	0.1212	-0.3617	1.4734	0.1264	-0.1587	-0.027	0.3963	0.0784	0.0162	0.6383	-0.0975	0.6287	18.9609	-18.2452	12.1023
86	6.9948	3.4548	2.1357	3.2828	-2.4295	8.6516	-0.3179	-0.8537	0.3868	-0.1615	0.2146	0.0132	-0.2278	0.1141	0.0896	0.3612	0.0144	0.1139	0.5869	-0.1762	0.6418	18.7616	-16.0618	18.1691
87	5.844	0.7591	2.3644	3.8785	5.2743	7.4881	1.5612	-0.0902	2.3446	-0.271	-1.1489	2.7912	-2.6094	-0.4464	-0.372	1.081	0.0014	0.1956	0.5672	-0.1891	1.1999	28.7019	3.438	13.8785

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 7 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 25 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 52 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 53 through 79 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 94 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 95 through 105 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 106 through 111 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 18 through 28 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 29 through 39 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 40 through 64 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 65 through 73 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 74 through 83 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 84 through 91 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 92 through 100 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 101 through 113 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 114 through 120 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 31 through 49 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 50 through 62 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 63 through 70 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 71 through 82 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 83 through 110 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 111 through 118 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 119 through 139 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 140 through 146 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1 through 7 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 8 through 18 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 19 through 25 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 26 through 36 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 37 through 52 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 53 through 65 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 66 through 79 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 80 through 94 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 95 through 105 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 106 through 111 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 1 through 17 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 18 through 28 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 29 through 39 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 40 through 51 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 52 through 60 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 61 through 67 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 68 through 120 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 31 through 49 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 50 through 70 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 71 through 110 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 111 through 118 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 119 through 139 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 140 through 146 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 1 through 9 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 10 through 18 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 19 through 36 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 37 through 52 )
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 53 through 65 )
54	X-RAY DIFFRACTION	54	chain 'G' and (resid 66 through 79 )
55	X-RAY DIFFRACTION	55	chain 'G' and (resid 80 through 94 )
56	X-RAY DIFFRACTION	56	chain 'G' and (resid 95 through 106 )
57	X-RAY DIFFRACTION	57	chain 'G' and (resid 107 through 111 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 1 through 17 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 18 through 39 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 40 through 51 )
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 52 through 57 )
62	X-RAY DIFFRACTION	62	chain 'H' and (resid 58 through 64 )
63	X-RAY DIFFRACTION	63	chain 'H' and (resid 65 through 73 )
64	X-RAY DIFFRACTION	64	chain 'H' and (resid 74 through 83 )
65	X-RAY DIFFRACTION	65	chain 'H' and (resid 84 through 100 )
66	X-RAY DIFFRACTION	66	chain 'H' and (resid 101 through 120 )
67	X-RAY DIFFRACTION	67	chain 'I' and (resid 31 through 49 )
68	X-RAY DIFFRACTION	68	chain 'I' and (resid 50 through 82 )
69	X-RAY DIFFRACTION	69	chain 'I' and (resid 83 through 110 )
70	X-RAY DIFFRACTION	70	chain 'I' and (resid 111 through 146 )
71	X-RAY DIFFRACTION	71	chain 'J' and (resid 1 through 9 )
72	X-RAY DIFFRACTION	72	chain 'J' and (resid 10 through 24 )
73	X-RAY DIFFRACTION	73	chain 'J' and (resid 25 through 36 )
74	X-RAY DIFFRACTION	74	chain 'J' and (resid 37 through 65 )
75	X-RAY DIFFRACTION	75	chain 'J' and (resid 66 through 94 )
76	X-RAY DIFFRACTION	76	chain 'J' and (resid 95 through 111 )
77	X-RAY DIFFRACTION	77	chain 'K' and (resid 1 through 17 )
78	X-RAY DIFFRACTION	78	chain 'K' and (resid 18 through 39 )
79	X-RAY DIFFRACTION	79	chain 'K' and (resid 40 through 60 )
80	X-RAY DIFFRACTION	80	chain 'K' and (resid 61 through 67 )
81	X-RAY DIFFRACTION	81	chain 'K' and (resid 68 through 120 )
82	X-RAY DIFFRACTION	82	chain 'L' and (resid 31 through 82 )
83	X-RAY DIFFRACTION	83	chain 'L' and (resid 83 through 104 )
84	X-RAY DIFFRACTION	84	chain 'L' and (resid 105 through 118 )
85	X-RAY DIFFRACTION	85	chain 'L' and (resid 119 through 132 )
86	X-RAY DIFFRACTION	86	chain 'L' and (resid 133 through 139 )
87	X-RAY DIFFRACTION	87	chain 'L' and (resid 140 through 146 )

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