PDB-5ggr: PD-1 in complex with nivolumab Fab

ID or keywords:

Entry

Database: PDB / ID: 5ggr

Title

PD-1 in complex with nivolumab Fab

Components

Programmed cell death protein 1
heavy chain
light chain

Keywords

IMMUNE SYSTEM / antibody

Function / homology

Function and homology information

negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of T cell activation / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / negative regulation of T cell receptor signaling pathway / negative regulation of inflammatory response / transmembrane signaling receptor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.3 Å

Authors

Heo, Y.S.

Citation

Journal: Nat Commun / Year: 2016
Title: Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy
Authors: Lee, J.Y. / Lee, H.T. / Shin, W. / Chae, J. / Choi, J. / Kim, S.H. / Lim, H. / Won Heo, T. / Park, K.Y. / Lee, Y.J. / Ryu, S.E. / Son, J.Y. / Lee, J.U. / Heo, Y.S.

History

Deposition	Jun 16, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ggr.cif.gz	419.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggr.ent.gz	347.3 KB	Display	PDB format
PDBx/mmJSON format	5ggr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggr ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggr	HTTPS FTP

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Related structure data

Related structure data	5ggqC 5ggsC 5ggtC 5gguC 5ggvC C: citing same article (ref.)
Similar structure data	5wt9-d 6uta-2 6nmu-1 4tsc-d 5x8l-1 4ttd-2 6u9s-1 6nmr-4 4tsb-d 6h5n-1 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

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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: heavy chain

B: light chain

H: heavy chain

L: light chain

Y: Programmed cell death protein 1

Z: Programmed cell death protein 1

124 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: heavy chain

B: light chain

Y: Programmed cell death protein 1

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

2

H: heavy chain

L: light chain

Z: Programmed cell death protein 1

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

Unit cell

Length a, b, c (Å)	91.290, 48.612, 134.904
Angle α, β, γ (deg.)	90.00, 102.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	heavy chain Mass: 24275.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody	light chain Mass: 23395.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein	Programmed cell death protein 1 / hPD-1 Mass: 14083.601 Da / Num. of mol.: 2 / Fragment: UNP residues 26-150 / Mutation: C93S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q15116
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: 2.37 Å³/Da / Density % sol: 48.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 17556 / % possible obs: 99 % / Redundancy: 3.4 % / Net I/σ(I): 6.9

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 3.3→29.752 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2679	897	5.11 %
R_work	0.2215	-	-
obs	0.2239	17553	98.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.3→29.752 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8256	0	0	0	8256

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8452
X-RAY DIFFRACTION	f_angle_d	1.286	11491
X-RAY DIFFRACTION	f_dihedral_angle_d	15.873	3058
X-RAY DIFFRACTION	f_chiral_restr	0.049	1282
X-RAY DIFFRACTION	f_plane_restr	0.007	1495

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 (%)
3.3001-3.5066	0.3019	153	0.2351	2786	X-RAY DIFFRACTION	100
3.5066-3.7768	0.3489	147	0.235	2768	X-RAY DIFFRACTION	99
3.7768-4.156	0.2384	148	0.2272	2761	X-RAY DIFFRACTION	99
4.156-4.7553	0.2735	139	0.1981	2765	X-RAY DIFFRACTION	98
4.7553-5.9831	0.2218	167	0.2096	2785	X-RAY DIFFRACTION	99
5.9831-29.7528	0.2376	143	0.2288	2791	X-RAY DIFFRACTION	95

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	0.7874	-0.5359	-0.0819	0.6602	-0.3574	0.412	0.2508	-0.5847	0.5444	-0.6241	0.2099	0.0544	-0.3959	0.4871	0.0347	-0.4705	0.2153	0.7862	0.3448	-0.3216	-0.0622	44.2375	5.7728	4.8154
2	1.2423	-0.2997	0.041	1.5134	0.1728	0.4519	0.0511	-0.2989	0.1976	1.1842	-0.9333	-1.2317	-0.5038	0.5542	0.0696	-0.235	0.2603	0.5289	0.1102	-0.1871	-0.0863	48.0585	0.1875	2.3375
3	0.1865	-0.1827	0.354	0.8459	-0.2221	0.6499	-0.1467	0.1443	-0.2635	0.1519	-0.2459	0.6298	0.0791	-0.0497	-0.0441	0.2258	0.1086	0.0163	0.3606	0.2203	-0.2641	39.6033	-5.6522	9.7072
4	3.0697	0.1527	0.3929	1.0273	0.2152	0.805	-0.0013	-0.4869	-0.1625	-0.2355	0.4721	0.5908	0.6718	-0.0183	-0.1465	0.3658	0.252	0.1124	0.4632	-0.2204	0.1236	48.1586	-11.6022	3.247
5	1.6043	-0.4802	0.0301	0.8794	0.4261	0.9695	0.462	0.1385	-0.4084	-0.1941	-0.0545	-0.1974	0.1204	-0.1197	-0.0834	0.3201	0.066	0.0979	0.1783	0.0141	0.2555	44.1588	-1.9002	5.5544
6	0.4111	-0.62	-0.5501	1.7105	0.3891	0.7742	0.2001	-0.1868	0.0648	-0.4845	0.2368	0.3711	-0.2133	0.0371	-0.0957	0.2827	0.0196	0.0362	0.4656	0.0568	0.197	27.7704	6.3845	-2.3337
7	0.9977	-0.109	-0.0003	1.2614	0.8166	1.1278	0.4638	-0.3514	-0.1342	0.1242	-0.3569	-0.2911	0.0311	0.2192	0.0268	0.3174	0.0031	0.2329	0.3123	-0.1255	-0.0042	15.0345	18.173	9.3254
8	0.7599	-0.2182	-0.0971	1.4989	0.5942	1.9368	0.1132	-0.2036	-0.1415	0.0573	-0.3054	0.4073	0.1171	-0.2563	0.0729	0.369	-0.0238	-0.1481	0.238	0.0126	0.2559	19.045	10.1877	9.0876
9	0.1463	0.4198	-0.1568	0.8762	-0.1776	1.2201	0.2656	-0.4484	0.3581	0.1762	0.2029	-0.1109	-0.3912	0.0175	-0.1741	0.2117	0.053	0.0141	0.4624	0.0081	0.2425	15.3798	23.47	10.7018
10	0.0336	0.1249	0.0353	0.5443	-0.1777	0.8874	0.2892	-0.3395	0.1888	0.582	0.0543	-0.2588	-0.5635	-0.2516	-0.1377	0.505	0.0473	-0.1035	0.31	0.1217	0.2069	12.8876	25.1572	4.7922
11	1.2572	-1.216	-0.331	2.3678	0.7929	0.2313	-0.3255	-0.2725	-0.0233	0.4906	0.5203	0.0779	0.3594	0.3513	-0.0427	0.4403	-0.1524	0.0431	0.3506	0.0649	0.2767	33.778	-10.3374	27.766
12	1.242	-0.2037	0.3036	0.3498	-0.4289	1.1856	0.0752	-0.1734	0.0762	-0.0101	-0.0906	0.0447	0.019	-0.1651	-0.0589	0.301	0.0337	0.0096	0.2811	0.0477	0.232	40.4701	-3.1054	27.8066
13	0.4736	-1.1765	-1.0266	2.6779	2.2279	1.8907	0.4428	0.1771	-0.9713	0.0303	0.3531	0.5375	0.3082	0.3616	0.1187	0.3216	-0.1009	-0.0516	0.3761	0.243	0.0893	39.5958	-12.7817	16.959
14	0.2908	-0.0019	0.149	0.0036	-0.0155	0.0882	-0.0187	-0.1665	-0.3331	0.463	-0.1575	-0.3183	0.2871	-0.2965	0.0573	0.285	0.011	0.0818	0.3931	-0.1084	0.3202	20.2713	5.7452	31.1876
15	1.3421	-0.2089	0.8234	0.744	-0.0716	2.0536	0.3322	-0.212	-0.6106	0.3812	0.0972	0.6644	0.3462	-0.6068	-0.1482	0.1882	-0.0797	0.0804	0.641	0.0278	0.4504	6.461	6.5897	13.012
16	3.2707	-0.3489	1.5322	1.5246	-0.0601	3.5159	-0.3475	0.002	-0.1531	-0.1012	0.2214	0.3852	-0.4731	-0.0279	-0.0505	0.2443	0.0092	-0.0229	0.1614	0.0069	0.3567	10.5329	7.5801	13.6184
17	1.3437	-0.4235	1.8903	0.7981	-0.5218	3.374	0.4508	-0.4355	-0.7573	0.0715	-0.7416	-0.0227	-0.1206	-0.4808	0.027	0.1927	-0.1511	0.1478	0.5436	0.2534	0.5772	1.0024	5.7171	19.7912
18	1.2605	0.0962	-0.1981	1.7102	0.7136	1.2895	-0.2319	-0.0854	-0.0266	0.2634	0.0163	0.2776	0.0372	-0.0813	0.2658	0.2948	0.0194	0.0131	0.2722	-0.031	0.2775	-12.9968	-23.8993	60.7347
19	0.612	0.5493	-0.0692	0.7676	-0.2093	1.0912	-0.2151	-0.4478	-0.0055	0.0561	0.2855	-0.2772	0.2371	-0.2314	-0.0438	0.3429	0.0635	0.0191	0.1596	0.0418	0.2479	-14.0042	-32.45	63.0754
20	6.2487	0.3752	4.1976	1.7045	0.2253	5.2262	-0.2124	-0.2111	-0.0682	-0.0563	0.0895	0.3577	-0.5908	-0.1141	0.1362	0.274	-0.0142	0.0466	0.2208	-0.0246	0.2305	-12.3654	-23.9036	54.6177
21	0.6358	0.2755	0.7079	0.382	0.3366	0.7357	-0.3685	-0.2031	-0.0547	0.1769	0.4053	-0.4741	-0.4357	0.3666	-0.0422	0.1548	0.0985	-0.1406	0.3765	-0.1012	0.4387	16.1921	-10.9395	62.0986
22	0.6124	-0.3222	-0.4153	0.3354	-0.058	1.8001	0.2805	-0.1649	-0.0857	0.0805	-0.2543	-0.1324	-0.5456	0.3124	-0.1801	0.3397	0.0082	-0.0195	0.254	-0.024	0.3321	14.5248	-5.3556	57.3034
23	0.952	1.1267	-0.4541	2.1462	-0.2041	0.5474	-0.3191	0.2764	-0.3641	-0.3502	0.1835	-0.1312	-0.2722	0.3478	-0.0469	0.225	0.1478	0.0781	0.3475	-0.0073	0.2799	-2.5346	-34.726	38.1895
24	1.2397	0.1824	0.2262	0.6204	-0.2121	0.872	-0.0373	0.2026	0.032	-0.077	0.0954	0.0163	0.1116	0.1081	-0.094	0.341	0.0401	0.0193	0.2846	-0.0558	0.342	-1.2727	-25.0822	41.962
25	1.385	-0.6034	1.1985	0.4278	-0.8552	1.8341	-0.1327	0.2498	-0.4256	0.3235	-0.5494	-0.0221	0.7588	0.2164	0.0666	0.337	-0.0057	0.0902	0.3467	0.1623	0.3701	22.2391	-18.82	48.9433
26	1.1978	0.4325	0.3885	0.6439	-0.0453	1.3014	0.2594	0.3983	-0.1494	0.2106	-0.118	0.0351	0.4549	0.6002	0.0165	0.3467	0.0184	0.0489	0.4274	-0.0331	0.3727	25.5486	-18.8442	50.7353
27	0.1533	-0.2881	0.4129	0.9627	-0.2675	1.9413	0.2738	0.2008	-0.0841	-0.0072	0.0005	-0.2688	-0.2932	-0.2876	-0.1423	0.3127	-0.0778	0.0891	0.3816	-0.0699	0.2847	71.8582	-9.2065	32.2808
28	2.59	0.3439	0.1437	1.989	-0.6991	2.3742	0.1099	0.1964	0.451	-0.0184	-0.0981	0.1409	-0.0341	0.0668	0.0805	0.4224	0.0127	-0.0806	0.2366	-0.0063	0.4094	68.346	-0.7772	34.6567
29	0.7666	-0.2873	0.6115	0.5583	-0.0611	0.7236	-0.3775	-0.1195	0.1797	-0.0648	0.3769	-0.2952	0.4587	0.7663	-0.1023	0.2709	-0.058	0.0513	0.1271	0.0345	0.2403	68.0259	-8.3496	38.7632
30	2.8265	1.8223	3.0922	1.1909	2.0541	5.6955	0.4342	0.0999	-0.1305	0.3983	-0.2663	-0.5157	-0.0574	0.1909	-0.0218	0.2652	0.1769	-0.0646	0.1387	0.1089	0.6142	-31.6935	-34.5983	48.0704
31	0.5103	0.2138	1.0587	0.3462	0.1199	2.2108	-0.1193	-0.0187	0.0939	0.14	0.0918	0.4203	0.2487	-0.0386	-0.0677	0.2992	0.0813	-0.0597	0.3407	0.0558	0.4367	-46.9041	-32.682	23.337
32	2.7328	0.0955	-0.3438	2.3535	0.804	2.2604	-0.0058	-0.016	0.2477	0.2051	-0.0359	0.0503	-0.1091	0.1839	-0.0262	0.2496	0.0474	-0.0491	0.2112	0.0545	0.3021	-37.0077	-24.8133	31.5309
33	0.3774	0.2665	0.0838	0.6622	-0.1203	0.9756	0.0705	-0.1694	0.1771	-0.0985	0.1454	-0.1304	0.5598	0.0628	0.007	0.2184	0.059	-0.0059	0.2541	-0.0353	0.3159	-36.4987	-32.5134	27.1012

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 51 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 52 through 73 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 106 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 107 through 119 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 120 through 159 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 177 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 178 through 204 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 205 through 213 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 90 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 91 through 102 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 103 through 113 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 114 through 160 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 161 through 190 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 191 through 212 )
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 2 through 44 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 45 through 91 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 92 through 109 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 110 through 135 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 136 through 213 )
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 1 through 33 )
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 34 through 126 )
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 127 through 150 )
26	X-RAY DIFFRACTION	26	chain 'L' and (resid 151 through 212 )
27	X-RAY DIFFRACTION	27	chain 'Y' and (resid 27 through 49 )
28	X-RAY DIFFRACTION	28	chain 'Y' and (resid 50 through 110 )
29	X-RAY DIFFRACTION	29	chain 'Y' and (resid 111 through 146 )
30	X-RAY DIFFRACTION	30	chain 'Z' and (resid 27 through 35 )
31	X-RAY DIFFRACTION	31	chain 'Z' and (resid 36 through 49 )
32	X-RAY DIFFRACTION	32	chain 'Z' and (resid 50 through 110 )
33	X-RAY DIFFRACTION	33	chain 'Z' and (resid 111 through 146 )

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