PDB-5ggq: Crystal structure of Nivolumab Fab fragment

ID or keywords:

Entry

Database: PDB / ID: 5ggq

Title

Crystal structure of Nivolumab Fab fragment

Components

nivolumab heavy chain
nivolumab light chain

Keywords

IMMUNE SYSTEM / therapeutic antibody

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: 1.9 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	Oct 16, 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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PDBx/mmCIF format	5ggq.cif.gz	180.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggq.ent.gz	144.7 KB	Display	PDB format
PDBx/mmJSON format	5ggq.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/5ggq ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggq	HTTPS FTP

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Related structure data

Related structure data	5ggrC 5ggsC 5ggtC 5gguC 5ggvC C: citing same article (ref.)
Similar structure data	3l7f-3 2g2r-1 5adp-d 1ucb-d 1jnl-d 3qnz-d 1a3l-d 6dc8-d 3g6j-4 2ajz-2 6rlm-5 5mp5-4 1nld-d 1mcp-d 6wj0-d 5l7x-d 4pb9-d 4z95-d 1mrc-d 1nd0-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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

L: nivolumab light chain

H: nivolumab heavy chain

47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.342, 88.342, 215.237
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	L-451- HOH
2	1	H-355- HOH
3	1	H-420- HOH

#1: Antibody	nivolumab light chain Mass: 23395.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody	nivolumab heavy chain Mass: 24275.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.54 Å³/Da / Density % sol: 51.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid, pH 3.5, 2.0 M ammonium sulfate

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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: 1.9→50 Å / Num. obs: 39971 / % possible obs: 99.8 % / Redundancy: 17.2 % / Net I/σ(I): 50.8

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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

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→31.178 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.31

	R_factor	Num. reflection	% reflection
R_free	0.2261	2006	5.02 %
R_work	0.1956	-	-
obs	0.1971	39971	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→31.178 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3187	0	0	311	3498

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3263
X-RAY DIFFRACTION	f_angle_d	1.152	4437
X-RAY DIFFRACTION	f_dihedral_angle_d	14.111	1165
X-RAY DIFFRACTION	f_chiral_restr	0.044	501
X-RAY DIFFRACTION	f_plane_restr	0.005	569

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 (%)
1.9004-1.9479	0.2522	144	0.2082	2615	X-RAY DIFFRACTION	99
1.9479-2.0005	0.2481	141	0.1946	2658	X-RAY DIFFRACTION	100
2.0005-2.0594	0.2111	154	0.1916	2650	X-RAY DIFFRACTION	100
2.0594-2.1259	0.2086	144	0.1786	2662	X-RAY DIFFRACTION	100
2.1259-2.2018	0.2487	126	0.1816	2685	X-RAY DIFFRACTION	100
2.2018-2.2899	0.2209	114	0.1858	2686	X-RAY DIFFRACTION	100
2.2899-2.3941	0.2744	141	0.1958	2691	X-RAY DIFFRACTION	100
2.3941-2.5203	0.2171	143	0.1961	2681	X-RAY DIFFRACTION	100
2.5203-2.6781	0.2308	165	0.1977	2683	X-RAY DIFFRACTION	100
2.6781-2.8848	0.2156	139	0.2018	2695	X-RAY DIFFRACTION	100
2.8848-3.1748	0.2239	147	0.1974	2735	X-RAY DIFFRACTION	100
3.1748-3.6336	0.2	136	0.188	2755	X-RAY DIFFRACTION	100
3.6336-4.5757	0.1982	152	0.1783	2795	X-RAY DIFFRACTION	100
4.5757-31.1819	0.2632	160	0.2222	2974	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	2.7291	-0.1151	1.0066	0.9442	0.2384	1.4169	-0.0279	0.0115	-0.1989	-0.0871	0.0361	-0.0176	0.0804	0.013	0.0079	0.1701	0.0054	-0.0011	0.1438	0.0073	0.118	19.1334	17.4254	104.4588
2	1.4328	1.301	0.6237	1.7704	1.287	1.0291	-0.1387	0.1429	0.2986	-0.2204	0.0175	0.2645	-0.207	0.0827	0.0909	0.2373	-0.0092	-0.0629	0.1313	0.0457	0.1812	20.9121	37.8986	108.8221
3	4.2389	-1.3356	-0.1052	6.1486	0.7261	1.5376	-0.031	-0.2281	0.4341	-0.1656	0.0296	0.5346	-0.1083	-0.2904	0.0262	0.1509	-0.0227	-0.0428	0.2464	-0.0002	0.2649	22.9651	47.0069	118.9072
4	5.6072	1.9414	-1.1854	2.0128	2.3625	0.2177	0.5318	-0.0234	-0.463	0.0092	0.019	1.0626	-0.0012	-0.1385	-0.1118	0.1723	0.4328	-0.3342	-0.9976	-0.1508	1.0335	17.6788	64.2511	118.3226
5	2.9042	-0.9703	0.3177	8.1829	-0.003	3.161	-0.0479	-0.1582	0.6881	-0.2099	-0.1492	0.4919	-0.2666	-0.2543	0.1288	0.2544	0.0081	-0.0347	0.1794	-0.057	0.3147	28.7386	55.059	124.2921
6	3.8105	-0.9374	-0.739	3.3008	1.3965	3.6291	0.2109	0.4114	0.0814	-0.249	-0.2473	-0.2877	-0.1259	0.2285	0.0354	0.1816	0.0198	-0.0207	0.2687	0.0272	0.1255	10.3397	33.1233	84.2655
7	4.1031	1.7437	3.6813	4.3775	3.2423	9.2241	0.078	0.0077	-0.0637	0.1931	-0.0552	-0.0683	0.3648	0.0391	0.0589	0.103	0.0245	-0.009	0.1022	0.0178	0.1109	6.9018	24.571	90.7338
8	5.044	-0.0562	-2.8038	2.8834	-0.3848	6.3262	0.1691	0.5355	-0.1576	-0.2169	-0.1454	0.0275	0.0661	-0.143	-0.0441	0.1426	0.045	-0.0282	0.177	-0.0375	0.1617	1.3329	25.976	85.0061
9	2.4304	0.7218	1.0063	1.5628	0.245	2.3342	-0.0561	0.1088	0.3452	0.1265	-0.068	-0.1079	-0.1363	0.0631	0.058	0.1341	-0.0005	-0.032	0.1552	0.02	0.1457	7.3538	35.2548	91.6452
10	0.3037	0.7237	-0.0568	2.7921	0.4563	0.3486	0.9488	-0.0285	-0.5933	-0.5318	0.1346	0.3039	0.7571	0.065	-0.7268	0.8068	-0.1393	-0.3017	0.4245	0.2442	0.6711	30.4088	61.1326	108.9797
11	1.6905	0.2921	1.9619	1.5506	0.3336	2.2692	-0.4683	0.6827	0.7973	-0.197	0.1434	0.2088	-0.7509	0.4132	0.3136	0.4991	-0.1752	-0.2047	0.3779	0.166	0.4437	22.4616	52.602	101.6655

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 75 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 76 through 137 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 138 through 174 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 175 through 190 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 191 through 211 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 2 through 33 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 34 through 57 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 58 through 76 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 77 through 119 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 120 through 134 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 135 through 209 )

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