PDB-6bi0: Trastuzumab Fab N158A, D185A, K190A (Light Chain) Triple Mutant.

ID or keywords:

Entry

Database: PDB / ID: 6bi0

Title

Trastuzumab Fab N158A, D185A, K190A (Light Chain) Triple Mutant.

Components

Trastuzumab anti-HER2 Fab Heavy Chain
Trastuzumab anti-HER2 Fab Light Chain

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: 2.057 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 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6bi0.cif.gz	348.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bi/6bi0 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bi0	HTTPS FTP

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Related structure data

Related structure data	6bhzC 6bi2C 1n8zS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ysl-4 5xhf-1 6qcu-d 5wtg-1 2bmk-1 6ug9-1 4mhh-3 1l7i-d 5yfi-d 2fjf-1 6ug9-2 5nyx-3 4lex-d 2gcy-d 6u3z-2 3dro-d 2fjf-4 4at6-7 6tco-1 5dub-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 - HomologyF&H Search

Related structure data

6bhzC

6bi2C

1n8zS

C: citing same article (ref.)

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	#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

I: Trastuzumab anti-HER2 Fab Heavy Chain

M: Trastuzumab anti-HER2 Fab Light Chain

hetero molecules

95 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

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.501, 79.561, 85.511
Angle α, β, γ (deg.)	113.00, 93.18, 102.13
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 Mass: 23320.896 Da / Num. of mol.: 2 / Mutation: N158A, D185A, K190A 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.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.46 Å³/Da / Density % sol: 50.04 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM Tris-HCl, pH 7.0, 20% PEGMME 2000

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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: 2.05→50 Å / Num. obs: 51673 / % possible obs: 92 % / Redundancy: 2.3 % / B_iso Wilson estimate: 28.57 Å² / R_merge(I) obs: 0.077 / R_pim(I) all: 0.064 / R_rim(I) all: 0.101 / Χ²: 0.927 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.05→2.12 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.475 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 3475 / CC_1/2: 0.695 / R_pim(I) all: 0.388 / R_rim(I) all: 0.616 / Χ²: 0.735 / % possible all: 61.5

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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: 2.057→44.112 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.22

	R_factor	Num. reflection	% reflection
R_free	0.2295	2321	5 %
R_work	0.1987	-	-
obs	0.2002	46400	82.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 36 Å²

Refinement step

Cycle: LAST / Resolution: 2.057→44.112 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6416	0	24	552	6992

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6687
X-RAY DIFFRACTION	f_angle_d	0.765	9116
X-RAY DIFFRACTION	f_dihedral_angle_d	13.816	3995
X-RAY DIFFRACTION	f_chiral_restr	0.047	1026
X-RAY DIFFRACTION	f_plane_restr	0.004	1165

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 (%)
2.057-2.0987	0.3172	48	0.2801	848	X-RAY DIFFRACTION	27
2.0987-2.1443	0.3284	70	0.2746	1160	X-RAY DIFFRACTION	37
2.1443-2.1942	0.2765	72	0.2619	1466	X-RAY DIFFRACTION	47
2.1942-2.2491	0.2971	107	0.2545	1760	X-RAY DIFFRACTION	57
2.2491-2.3099	0.2897	104	0.263	2247	X-RAY DIFFRACTION	72
2.3099-2.3778	0.2989	164	0.2461	2699	X-RAY DIFFRACTION	86
2.3778-2.4546	0.2874	147	0.2466	2977	X-RAY DIFFRACTION	95
2.4546-2.5423	0.2875	184	0.24	3044	X-RAY DIFFRACTION	97
2.5423-2.6441	0.2655	158	0.2388	3065	X-RAY DIFFRACTION	98
2.6441-2.7644	0.2486	148	0.2176	3121	X-RAY DIFFRACTION	98
2.7644-2.9101	0.2491	157	0.2117	3070	X-RAY DIFFRACTION	98
2.9101-3.0924	0.2424	192	0.2097	3043	X-RAY DIFFRACTION	99
3.0924-3.3311	0.2188	162	0.2029	3081	X-RAY DIFFRACTION	99
3.3311-3.6661	0.2114	145	0.1798	3129	X-RAY DIFFRACTION	99
3.6661-4.1963	0.1864	137	0.1734	3150	X-RAY DIFFRACTION	99
4.1963-5.2855	0.1796	163	0.1493	3108	X-RAY DIFFRACTION	99
5.2855-44.11	0.2031	163	0.1801	3111	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	3.1852	0.8356	-0.3761	4.1618	-1.3064	3.059	-0.007	0.0192	0.0844	-0.098	-0.0147	-0.0756	-0.2497	0.3158	0.0077	0.1162	0.0309	0.0071	0.1587	-0.0061	0.1116	16.0665	24.1384	-20.8652
2	2.1845	-0.3124	0.7109	2.6087	-0.4212	2.3896	0.0183	0.0877	0.0872	-0.2886	0.0089	0.5462	0.0016	-0.184	-0.0351	0.1087	0.0333	-0.0358	0.1653	-0.0199	0.1447	7.8675	23.5812	-20.7962
3	3.6583	1.6163	-0.4163	2.1651	-0.5491	5.7023	-0.1589	0.3786	0.4575	-0.3519	0.1557	-0.0158	-0.6889	0.1176	0.0548	0.251	0.0182	0.0174	0.2496	0.0255	0.1811	16.53	23.1018	-31.0046
4	2.2743	-1.2858	0.6887	3.3258	1.3751	1.593	0.0503	-0.0567	-0.2829	0.2288	0.0154	0.0627	0.1096	0.0347	0.03	0.1597	-0.0046	0.0012	0.1951	0.0062	0.1956	16.8681	7.4252	-9.0976
5	1.1251	-0.2275	-0.8096	2.6565	0.9613	2.2619	0.0681	0.0389	-0.123	0.2042	0.3953	-0.7569	0.1598	0.3796	-0.2934	0.2316	0.0516	-0.0663	0.2047	-0.0874	0.4453	32.6267	-3.731	-14.7698
6	2.0445	-0.82	-0.1162	4.0591	1.9813	6.453	-0.0912	0.2187	-0.1624	-0.2428	-0.1107	0.2439	0.4497	0.2118	0.1491	0.2833	0.0425	-0.0242	0.3385	-0.0313	0.1829	14.4608	12.9592	-42.222
7	1.3142	-0.8496	0.1946	4.8751	-0.432	3.3482	0.1284	-0.0439	-0.277	0.0203	0.1218	0.0221	0.3075	-0.1263	-0.1942	0.2744	0.0012	-0.0809	0.1431	0.0029	0.2941	24.3239	-14.0544	-22.798
8	1.4106	-0.5055	0.0525	4.4471	-0.5835	4.4173	0.023	0.0061	-0.3349	-0.1137	0.2028	0.0089	0.6236	-0.047	-0.1226	0.3349	0.0013	-0.0788	0.1589	-0.0188	0.3463	25.7747	-17.7185	-21.7469
9	3.378	0.3551	-0.0647	3.4687	-0.9855	3.8296	0.0524	0.0651	0.2214	-0.1555	-0.1103	0.3973	-0.4135	-0.3919	0.0247	0.1375	-0.004	0.0041	0.156	-0.0502	0.2088	27.6837	32.2279	-6.8807
10	2.1894	0.8161	-0.4201	4.133	-0.4573	3.4866	0.0744	-0.1745	0.0939	0.1392	-0.1965	-0.2598	-0.3563	0.3686	0.0998	0.1071	-0.0244	-0.0056	0.1495	-0.0069	0.1309	36.2068	31.69	-6.0114
11	1.9546	-0.5608	-0.1553	3.9358	-0.5708	2.9023	0.1351	0.0604	0.1516	-0.1885	-0.2178	0.8283	-0.8682	-0.4857	0.0327	0.3926	0.0392	0.0312	0.1785	-0.0737	0.2928	26.9823	37.0906	-0.3119
12	0.9634	0.9984	-1.5328	1.3698	-1.3258	3.3891	0.0157	-0.1774	-0.072	0.081	-0.0461	-0.0263	0.1031	-0.3917	0.0526	0.1598	-0.0459	-0.0161	0.3545	0.0313	0.1879	16.8225	12.6903	11.7374
13	2.052	-0.5895	-2.5513	0.8082	0.3674	3.1624	0.0014	0.1503	-0.1906	-0.0915	-0.1507	0.1159	-0.1701	-1.2177	0.1758	0.2168	-0.1026	-0.0267	0.6297	0.0366	0.2318	7.5144	10.7329	13.1325
14	1.6636	0.7605	2.0114	2.7467	1.0799	2.9855	-0.0366	-0.6511	-0.0825	0.803	0.07	0.0486	0.1716	0.3931	-0.1097	0.5875	-0.0694	0.0922	0.3083	-0.0673	0.2247	29.4938	40.7732	21.6262
15	1.3105	0.087	0.3564	3.0293	1.6131	3.4533	-0.0435	-0.3023	0.309	-0.0139	0.0387	0.283	-1.2573	0.3659	0.1665	0.6749	-0.1803	0.0776	0.3367	-0.1439	0.2128	29.5039	46.7205	12.6512
16	3.3963	-0.4958	-1.3793	2.5285	1.4095	3.3282	-0.2946	0.0526	0.1453	0.0542	0.3038	0.0167	-0.1015	0.2173	-0.017	0.432	-0.1208	0.0145	0.377	-0.1077	0.2308	29.6411	41.2786	12.4241
17	0.959	0.3693	-1.184	0.2745	-0.5343	1.4376	0.3675	-0.1415	0.1908	0.403	-0.3913	0.1471	-0.2475	-0.3373	-0.2504	0.6697	-0.2639	0.4176	0.5018	-0.0613	0.1596	18.511	32.0086	28.1968
18	3.1176	0.0146	-2.0089	5.0857	0.7666	5.9662	-0.0521	0.2836	-0.2617	0.4418	-0.2038	-0.2318	1.3644	-0.5822	0.2603	0.539	-0.1847	0.0632	0.4056	0.0657	0.2292	13.9977	2.3735	21.7575
19	1.9854	-0.4101	-0.4804	8.3632	0.2228	1.9219	0.1605	-0.5644	0.042	0.5034	-0.2148	-0.8224	-0.1575	0.2448	0.0942	0.3568	-0.1671	-0.0133	0.439	0.0662	0.2545	19.907	14.6446	29.0572
20	0.4696	1.2891	-1.733	3.7479	-4.719	7.0306	0.0467	-1.1357	-0.5408	0.5132	-0.7271	-0.617	0.1284	0.5099	0.5487	0.4244	-0.1453	-0.1001	0.7479	0.2459	0.3664	25.9472	8.0863	29.0619
21	3.0862	-0.4905	-1.8836	9.0492	-1.0168	3.403	0.2094	-0.5292	-0.1562	-0.9848	-0.2518	-0.3521	0.106	0.209	0.0181	0.2343	-0.0602	-0.0205	0.3353	0.047	0.1438	18.6102	13.0298	23.8218
22	1.4563	-0.0402	-0.1531	3.6527	2.7735	2.1885	-0.1255	-0.4122	-0.1715	0.9928	-0.1672	-0.1296	-0.2701	0.9126	-0.003	0.7277	-0.224	-0.1044	0.563	0.0559	0.2153	16.5625	7.6495	34.8682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 2 through 39 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 40 through 91 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 92 through 113 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 114 through 126 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 127 through 220 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 2 through 101 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 102 through 163 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 164 through 213 )
9	X-RAY DIFFRACTION	9	chain 'I' and (resid 1 through 39 )
10	X-RAY DIFFRACTION	10	chain 'I' and (resid 40 through 91 )
11	X-RAY DIFFRACTION	11	chain 'I' and (resid 92 through 113 )
12	X-RAY DIFFRACTION	12	chain 'I' and (resid 114 through 182 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 183 through 220 )
14	X-RAY DIFFRACTION	14	chain 'M' and (resid 2 through 18 )
15	X-RAY DIFFRACTION	15	chain 'M' and (resid 19 through 75 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 76 through 101 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 102 through 113 )
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 114 through 128 )
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 129 through 150 )
20	X-RAY DIFFRACTION	20	chain 'M' and (resid 151 through 163 )
21	X-RAY DIFFRACTION	21	chain 'M' and (resid 164 through 188 )
22	X-RAY DIFFRACTION	22	chain 'M' and (resid 189 through 214 )

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