PDB-6bhz: Trastuzumab Fab D185A (Light Chain) Mutant.

ID or keywords:

Entry

Database: PDB / ID: 6bhz

Title

Trastuzumab Fab D185A (Light Chain) Mutant.

Components

Trastuzumab Anti-HER2 Fab Heavy Chain
Trastuzumab Anti-HER2 Fab Light Chain D185A

Keywords

IMMUNE SYSTEM / Fab / immunoglobulin / mutant

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

DiDonato, M. / Spraggon, G.

Citation

Journal: Chembiochem / Year: 2018
Title: Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.
Authors: Pham, G.H. / Ou, W. / Bursulaya, B. / DiDonato, M. / Herath, A. / Jin, Y. / Hao, X. / Loren, J. / Spraggon, G. / Brock, A. / Uno, T. / Geierstanger, B.H. / Cellitti, S.E.

History

Deposition	Oct 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2	Apr 25, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 4, 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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PDBx/mmCIF format	6bhz.cif.gz	364.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6bhz.ent.gz	296.8 KB	Display	PDB format
PDBx/mmJSON format	6bhz.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/bh/6bhz ftp://data.pdbj.org/pub/pdb/validation_reports/bh/6bhz	HTTPS FTP

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Related structure data

Related structure data	6bi0C 6bi2C 1n8zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5tdp-1 4pb0-d 6c6x-2 6bi0-2 5l7x-d 7k8p-d 6dwa-1 5tdn-2 5dsc-1 3g6j-4 5nbw-1 1mex-d 2hff-1 1mcp-d 6n16-3 1mam-d 6dc8-d 1mim-d 6ute-3 5x5x-d 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 - HomologyF&H Search

Related structure data

6bi0C

6bi2C

1n8zS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: Trastuzumab Anti-HER2 Fab Heavy Chain

L: Trastuzumab Anti-HER2 Fab Light Chain D185A

I: Trastuzumab Anti-HER2 Fab Heavy Chain

M: Trastuzumab Anti-HER2 Fab Light Chain D185A

hetero molecules

95.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: Trastuzumab Anti-HER2 Fab Heavy Chain

L: Trastuzumab Anti-HER2 Fab Light Chain D185A

hetero molecules

defined by author&software
Evidence: homology
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: Trastuzumab Anti-HER2 Fab Heavy Chain

M: Trastuzumab Anti-HER2 Fab Light Chain D185A

hetero molecules

defined by author&software
Evidence: homology
47.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.571, 79.506, 85.591
Angle α, β, γ (deg.)	113.18, 93.19, 102.52
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Trastuzumab Anti-HER2 Fab Heavy Chain Mass: 23988.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Trastuzumab Anti-HER2 Fab Light Chain D185A Mass: 23422.021 Da / Num. of mol.: 2 / Mutation: D185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.45 Å³/Da / Density % sol: 49.86 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 200 mM di-Ammonium Tartrate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2017
Radiation	Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97648 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. obs: 88658 / % possible obs: 97.5 % / Redundancy: 2.4 % / B_iso Wilson estimate: 18.3 Å² / R_pim(I) all: 0.033 / R_rim(I) all: 0.051 / R_sym value: 0.039 / Χ²: 0.886 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.75→1.79 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5727 / CC_1/2: 0.799 / R_rim(I) all: 0.446 / Χ²: 0.86 / % possible all: 95.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1N8Z

1n8z

Resolution: 1.75→42.271 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.07

	R_factor	Num. reflection	% reflection
R_free	0.1911	4188	4.74 %
R_work	0.1679	-	-
obs	0.169	88353	97.07 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→42.271 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6442	0	16	1006	7464

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6847
X-RAY DIFFRACTION	f_angle_d	0.842	9369
X-RAY DIFFRACTION	f_dihedral_angle_d	13.256	4122
X-RAY DIFFRACTION	f_chiral_restr	0.052	1054
X-RAY DIFFRACTION	f_plane_restr	0.006	1207

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 (%)
1.749-1.7688	0.2739	120	0.2396	2446	X-RAY DIFFRACTION	85
1.7688-1.7897	0.2897	154	0.2229	2646	X-RAY DIFFRACTION	93
1.7897-1.8115	0.2423	120	0.2124	2792	X-RAY DIFFRACTION	96
1.8115-1.8344	0.2445	114	0.2026	2840	X-RAY DIFFRACTION	96
1.8344-1.8585	0.1995	121	0.2009	2781	X-RAY DIFFRACTION	97
1.8585-1.884	0.2709	148	0.2038	2761	X-RAY DIFFRACTION	96
1.884-1.9109	0.2223	115	0.1907	2848	X-RAY DIFFRACTION	96
1.9109-1.9394	0.196	132	0.1851	2808	X-RAY DIFFRACTION	97
1.9394-1.9698	0.215	129	0.1815	2796	X-RAY DIFFRACTION	97
1.9698-2.002	0.1929	143	0.1752	2800	X-RAY DIFFRACTION	97
2.002-2.0366	0.2062	142	0.1756	2847	X-RAY DIFFRACTION	97
2.0366-2.0736	0.1819	122	0.1704	2759	X-RAY DIFFRACTION	97
2.0736-2.1135	0.1884	158	0.1698	2794	X-RAY DIFFRACTION	97
2.1135-2.1566	0.2002	150	0.1691	2813	X-RAY DIFFRACTION	98
2.1566-2.2035	0.2203	139	0.1768	2789	X-RAY DIFFRACTION	97
2.2035-2.2548	0.2266	152	0.1689	2839	X-RAY DIFFRACTION	98
2.2548-2.3111	0.2316	134	0.1844	2823	X-RAY DIFFRACTION	98
2.3111-2.3736	0.1915	163	0.1732	2829	X-RAY DIFFRACTION	98
2.3736-2.4435	0.2129	119	0.1779	2837	X-RAY DIFFRACTION	98
2.4435-2.5223	0.1969	131	0.1787	2838	X-RAY DIFFRACTION	98
2.5223-2.6125	0.2196	174	0.1771	2802	X-RAY DIFFRACTION	98
2.6125-2.717	0.1879	145	0.169	2840	X-RAY DIFFRACTION	98
2.717-2.8407	0.1919	154	0.1687	2810	X-RAY DIFFRACTION	98
2.8407-2.9904	0.175	147	0.1703	2896	X-RAY DIFFRACTION	99
2.9904-3.1777	0.2116	145	0.1722	2840	X-RAY DIFFRACTION	99
3.1777-3.423	0.1753	123	0.1626	2851	X-RAY DIFFRACTION	99
3.423-3.7672	0.179	168	0.1546	2830	X-RAY DIFFRACTION	99
3.7672-4.3119	0.1568	143	0.1446	2893	X-RAY DIFFRACTION	99
4.3119-5.4307	0.153	152	0.1322	2861	X-RAY DIFFRACTION	99
5.4307-42.2829	0.158	131	0.1621	2856	X-RAY DIFFRACTION	99

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	1.5149	1.2323	-0.464	3.3948	-0.9149	2.1311	0.0033	-0.0196	0.0183	-0.1508	-0.0513	-0.1031	-0.163	0.3251	0.0538	0.0894	0.0013	0.0013	0.1475	-0.0002	0.1025	16.9222	24.1712	-20.7988
2	1.4262	0.0481	-0.0101	1.7421	-0.3015	2.1363	-0.0163	0.0924	0.0568	-0.2603	-0.0175	0.1878	-0.0041	-0.051	0.0291	0.075	0.0141	-0.0116	0.1057	-0.0021	0.102	9.6062	23.3432	-22.1285
3	0.8111	-0.035	0.3767	1.2088	0.2577	0.5005	0.0419	0.0547	-0.1917	0.0597	0.1367	-0.1955	0.1317	0.0183	-0.1219	0.1287	0.0206	-0.0023	0.122	-0.0258	0.2009	25.7045	2.5408	-17.1508
4	1.389	-0.2776	-1.1996	1.0829	0.6332	1.5263	0.1013	-0.0678	-0.2094	0.2815	0.3703	-0.8131	0.3119	0.3521	-0.1544	0.1831	0.0952	-0.118	0.1987	-0.1406	0.5197	36.5349	-3.6481	-13.6852
5	5.0532	-1.883	-0.2538	3.3091	0.3594	2.1504	-0.0519	0.2156	-0.3118	-0.1243	-0.2018	0.2648	0.6416	-0.186	0.1247	0.375	-0.0039	-0.03	0.2293	-0.0189	0.1646	11.7783	6.5266	-43.4396
6	1.276	0.8224	-0.9391	2.375	0.4653	2.687	-0.0841	0.1236	0.1619	-0.2206	-0.0649	-0.136	0.1107	0.2757	0.1515	0.1796	0.0418	0.0066	0.1925	0.0093	0.1017	17.0812	17.3271	-40.7048
7	1.7119	-0.1744	-0.3925	1.8828	0.5619	3.2377	-0.0456	0.0005	0.0262	-0.186	-0.0498	-0.0268	0.3318	0.106	0.0381	0.2303	0.0495	-0.0196	0.215	-0.0352	0.1331	13.5562	12.9453	-41.8332
8	1.6755	-2.4514	0.3733	4.3851	-0.3764	0.0461	0.1571	0.3052	0.0836	-0.1839	-0.2128	-0.394	-0.1845	-0.043	-0.0053	0.4742	0.1109	0.0036	0.2011	-0.0056	0.1923	24.3672	-5.7965	-39.1091
9	1.2735	-0.1384	-0.3755	2.2731	-0.9004	3.015	0.0379	0.0059	-0.1966	0.2459	0.226	-0.344	-0.0119	-0.0402	-0.1718	0.3002	0.0312	-0.1273	0.0664	0.0198	0.2779	26.6029	-15.3444	-19.4045
10	0.8769	-0.1358	-0.2839	3.6497	-0.8766	2.555	0.0684	-0.0011	-0.158	-0.1543	0.0376	-0.0062	0.1286	0.0124	-0.111	0.2193	-0.0022	-0.084	0.1206	0.0055	0.2601	24.5957	-18.1247	-20.9635
11	1.8918	-1.1554	0.784	4.9785	-1.457	1.7208	-0.0349	-0.0464	0.0044	-0.0687	-0.0434	0.2873	-0.155	-0.1358	0.0649	0.0888	-0.0029	-0.0159	0.1116	-0.0199	0.1283	26.39	31.4003	-7.8922
12	1.373	0.1905	-0.2552	2.2448	-0.2937	1.856	-0.0064	-0.0655	0.076	0.1428	-0.074	0.0035	-0.2018	0.1235	0.0394	0.0695	-0.0176	-0.0081	0.0855	-0.0115	0.0954	33.675	33.1363	-4.0032
13	0.5004	0.4485	-0.7943	1.0841	-0.644	1.4556	-0.0045	-0.0662	-0.0219	0.062	0.0264	0.0353	0.0037	-0.2161	-0.0051	0.0983	-0.0142	0.0058	0.2517	0.0381	0.1468	15.9301	12.393	12.9082
14	5.2678	0.3532	-4.7128	0.7258	-0.594	4.0922	-0.1075	0.3104	0.0288	-0.0339	0.1196	0.108	0.1265	-0.5672	0.0548	0.132	-0.0432	0.0017	0.3423	0.0284	0.1652	7.1812	8.9781	9.9748
15	2.7536	0.9324	-0.3045	1.3095	-0.4975	2.0908	0.0038	-0.3672	-0.1214	0.3484	-0.0925	0.0808	0.1327	0.2238	0.049	0.4423	-0.0697	0.0346	0.3004	-0.0794	0.1865	30.2677	40.3311	20.8474
16	1.0464	-0.6344	-0.021	2.0735	0.7149	2.4734	0.0436	-0.2726	0.3443	0.1505	-0.1251	0.0737	-0.5475	0.1127	0.0811	0.3803	-0.0889	0.04	0.2072	-0.0824	0.2015	29.1387	46.5436	12.924
17	2.7588	-0.3462	-0.7124	2.3896	1.1061	3.2671	0.0992	-0.3144	0.19	0.26	-0.0922	0.0898	-0.2681	0.1699	0.0263	0.3223	-0.0772	0.0092	0.1976	-0.0546	0.1588	29.323	40.9069	12.8505
18	1.6404	1.8765	-2.1789	2.11	-2.4979	3.0137	0.1905	-0.0676	0.0167	0.193	-0.1139	-0.0427	-0.1418	0.1211	-0.0313	0.4232	-0.0686	0.1257	0.3312	-0.0504	0.2172	17.2119	31.0857	29.0288
19	2.9326	-1.3122	-1.794	5.3767	2.6297	4.691	0.1266	0.1423	-0.2902	0.001	-0.3055	0.0238	0.297	-0.414	0.102	0.2103	-0.0699	0.0238	0.2288	0.0426	0.1823	14.2135	2.0112	22.015
20	1.789	-0.9012	-0.1035	7.8542	1.3662	1.2651	0.224	-0.4293	0.0086	0.3645	-0.2236	-0.5647	-0.1348	0.1038	-0.0267	0.2458	-0.1094	-0.0022	0.295	0.0478	0.1678	19.8421	14.3695	29.2234
21	1.4932	0.6337	-0.7746	3.3417	0.0596	2.1163	0.1854	-0.3299	-0.1332	0.316	-0.32	-0.2003	-0.0343	0.1727	0.0684	0.1702	-0.0589	-0.0062	0.2734	0.0506	0.1478	21.0498	11.3113	25.6087
22	1.4329	0.2786	-0.4615	3.7466	-0.289	1.9087	0.1153	-0.2267	0.0236	0.6803	-0.2279	-0.0222	-0.1097	0.2562	0.0503	0.3162	-0.098	-0.0397	0.3159	0.0656	0.1558	16.7601	7.5116	35.072

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 39 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 40 through 103 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 104 through 182 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 183 through 220 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 25 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 26 through 61 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 62 through 101 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 102 through 113 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 114 through 150 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 151 through 213 )
11	X-RAY DIFFRACTION	11	chain 'I' and (resid 1 through 32 )
12	X-RAY DIFFRACTION	12	chain 'I' and (resid 33 through 113 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 114 through 195 )
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 196 through 220 )
15	X-RAY DIFFRACTION	15	chain 'M' and (resid 1 through 18 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 19 through 75 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 76 through 102 )
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 103 through 113 )
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 114 through 128 )
20	X-RAY DIFFRACTION	20	chain 'M' and (resid 129 through 150 )
21	X-RAY DIFFRACTION	21	chain 'M' and (resid 151 through 188 )
22	X-RAY DIFFRACTION	22	chain 'M' and (resid 189 through 214 )

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