PDB-5vh4: Crystal structure of Fab fragment of anti-TNFa antibody inflixima...

ID or keywords:

Entry

Database: PDB / ID: 5vh4

Title

Crystal structure of Fab fragment of anti-TNFa antibody infliximab in an I-centered orthorhombic crystal form

Components

Infliximab Fab Heavy Chain
Infliximab Fab Light Chain

Keywords

IMMUNE SYSTEM / antibody / Fab / biosimilar / infliximab / TNFa / anti-TNFa

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Mayclin, S.J. / Edwards, T.E. / Lerch, T.F. / Conlan, H. / Sharpe, P.

Citation

Journal: MAbs / Year: 2017
Title: Infliximab crystal structures reveal insights into self-association.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Lee, E. / Conlon, H.D. / Polleck, S. / Rouse, J.C. / Luo, Y. / Zou, Q.

History

Deposition	Apr 12, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2017	Group: Database references
Revision 1.2	Aug 2, 2017	Group: 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	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vh4.cif.gz	365.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5vh4.ent.gz	296.9 KB	Display	PDB format
PDBx/mmJSON format	5vh4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vh4_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5vh4_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5vh4_validation.xml.gz	42.2 KB	Display
Data in CIF	5vh4_validation.cif.gz	62.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/5vh4 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/5vh4	HTTPS FTP

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Related structure data

Related structure data	5vh3C 5vh5C 4g3yS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5mv3-8 5mv3-3 5k9j-d 5mv3-2 5mu0-1 1m7d-d 5b6f-2 3g6j-4 1rz8-2 1aj7-d 4yhi-2 2gcy-d 4r96-4 5b6f-3 6dwa-1 5mv3-7 4gaj-d 1bfo-1 2ajy-d 5mv4-8 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

5vh3C

5vh5C

4g3yS

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: Infliximab Fab Heavy Chain

L: Infliximab Fab Light Chain

A: Infliximab Fab Heavy Chain

B: Infliximab Fab Light Chain

hetero molecules

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

1

H: Infliximab Fab Heavy Chain

L: Infliximab Fab Light Chain

hetero molecules

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

2

A: Infliximab Fab Heavy Chain

B: Infliximab Fab Light Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.850, 93.610, 316.070
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	H-429- HOH
2	1	H-472- HOH
3	1	A-582- HOH

#1: Antibody	Infliximab Fab Heavy Chain Mass: 24356.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Infliximab Fab Light Chain Mass: 23460.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 854 / 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: 3.51 Å³/Da / Density % sol: 64.99 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Infliximab Fab at 10 mg/mL against 2.16 M sodium malonate, 10 mM NAD, crystal tracking ID 267666d9, unique puck ID sar8-4

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 91050 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.007 % / B_iso Wilson estimate: 25.28 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.081 / R_rim(I) all: 0.091 / Χ²: 0.953 / Net I/σ(I): 15.59

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	5.012	0.654	2.93	6634	0.803	0.73	99.9
2.05-2.11	5.03	0.534	3.59	6546	0.873	0.596	99.9
2.11-2.17	5.038	0.41	4.54	6334	0.92	0.458	99.9
2.17-2.24	5.035	0.338	5.39	6123	0.944	0.378	100
2.24-2.31	5.04	0.293	6.05	5964	0.945	0.327	99.9
2.31-2.39	5.041	0.258	6.71	5765	0.961	0.288	99.9
2.39-2.48	5.046	0.226	7.62	5581	0.968	0.252	99.8
2.48-2.58	5.043	0.186	8.91	5376	0.977	0.208	99.9
2.58-2.7	5.048	0.144	11.24	5164	0.986	0.161	99.9
2.7-2.83	5.035	0.112	13.63	4955	0.992	0.125	99.9
2.83-2.98	5.044	0.088	16.93	4700	0.994	0.098	99.9
2.98-3.16	5.015	0.065	21.81	4463	0.996	0.073	99.8
3.16-3.38	5.004	0.05	26.74	4198	0.998	0.056	99.9
3.38-3.65	4.97	0.043	31.08	3924	0.998	0.048	99.9
3.65-4	4.976	0.037	35.1	3608	0.998	0.041	99.8
4-4.47	4.942	0.031	40.13	3290	0.999	0.035	99.8
4.47-5.16	4.932	0.03	42.66	2911	0.999	0.033	99.6
5.16-6.32	4.916	0.03	39.9	2478	0.999	0.033	99.4
6.32-8.94	4.835	0.029	41.35	1939	0.999	0.033	98.7
8.94-50	4.437	0.026	46.2	1097	0.999	0.029	95.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
Coot		model building
PHENIX	dev_2229	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4g3y

4g3y

Resolution: 2→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.06

	R_factor	Num. reflection	% reflection
R_free	0.1865	4542	4.99 %
R_work	0.1579	-	-
obs	0.1594	91022	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 118.37 Å² / B_iso mean: 31.5958 Å² / B_iso min: 11.47 Å²

Refinement step

Cycle: final / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6570	0	108	854	7532
B_iso mean	-	-	72.94	38.89	-
Num. residues	-	-	-	-	868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6930
X-RAY DIFFRACTION	f_angle_d	0.864	9469
X-RAY DIFFRACTION	f_chiral_restr	0.055	1059
X-RAY DIFFRACTION	f_plane_restr	0.005	1209
X-RAY DIFFRACTION	f_dihedral_angle_d	13.468	4094

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0228	0.2314	155	0.2165	2836	2991	100
2.0228-2.0466	0.2324	141	0.2114	2840	2981	100
2.0466-2.0715	0.2556	143	0.208	2881	3024	100
2.0715-2.0978	0.2384	155	0.2042	2825	2980	100
2.0978-2.1254	0.2675	141	0.1942	2865	3006	100
2.1254-2.1545	0.2057	152	0.1782	2850	3002	100
2.1545-2.1853	0.2244	160	0.1762	2880	3040	100
2.1853-2.2179	0.2112	136	0.1793	2861	2997	100
2.2179-2.2525	0.1916	141	0.1713	2889	3030	100
2.2525-2.2895	0.2113	175	0.1708	2824	2999	100
2.2895-2.3289	0.2151	153	0.1776	2875	3028	100
2.3289-2.3713	0.1856	150	0.1663	2849	2999	100
2.3713-2.4169	0.179	148	0.1736	2857	3005	100
2.4169-2.4662	0.1941	137	0.1728	2889	3026	100
2.4662-2.5198	0.2497	152	0.1808	2864	3016	100
2.5198-2.5784	0.2329	156	0.1786	2850	3006	100
2.5784-2.6429	0.2218	155	0.1792	2868	3023	100
2.6429-2.7144	0.2226	158	0.1743	2877	3035	100
2.7144-2.7942	0.1857	147	0.1734	2875	3022	100
2.7942-2.8844	0.208	155	0.1731	2884	3039	100
2.8844-2.9875	0.211	137	0.1748	2900	3037	100
2.9875-3.1071	0.2101	156	0.1724	2914	3070	100
3.1071-3.2485	0.2052	152	0.1627	2865	3017	100
3.2485-3.4197	0.2165	169	0.1588	2881	3050	100
3.4197-3.6339	0.1746	162	0.1397	2913	3075	100
3.6339-3.9143	0.1614	145	0.1311	2899	3044	100
3.9143-4.308	0.1128	157	0.1181	2928	3085	100
4.308-4.9308	0.1025	126	0.1032	2965	3091	100
4.9308-6.2099	0.1536	152	0.1336	2963	3115	99
6.2099-46.8178	0.1728	176	0.1691	3013	3189	97

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	1.5593	0.5271	0.9536	1.4548	0.79	1.9201	0.0249	0.0915	0.0164	0.008	-0.0361	-0.0505	0.0192	0.1217	-0.0031	0.1447	-0.0044	-0.0081	0.1935	0.0172	0.1318	-10.8995	6.1932	11.0384
2	2.102	-0.0346	0.7506	0.7553	0.7804	1.1978	-0.1051	-0.3597	-0.2223	0.3141	0.1276	-0.1723	0.3016	0.2515	0.014	0.2654	0.072	-0.0013	0.313	0.0621	0.203	5.6223	-0.8349	35.2923
3	1.1063	0.9133	0.0128	3.8496	-0.7604	1.1172	-0.148	0.0369	-0.0083	-0.0796	0.1022	-0.2639	0.0333	0.1055	0.049	0.2421	0.047	0.0134	0.2491	0.0317	0.2283	6.1347	-6.9154	33.557
4	2.0801	-1.2878	1.167	2.6753	-1.275	3.4379	0.0221	-0.2597	-0.2606	0.2017	0.1071	0.1732	0.1627	-0.2656	-0.129	0.1682	-0.0321	0.0052	0.2176	0.0364	0.1668	-30.1219	-2.9208	26.5441
5	4.5501	0.3191	0.8405	2.7713	-0.1929	3.3996	0.1641	-0.0746	-0.4267	0.0991	-0.0861	-0.2267	0.1465	0.3698	-0.0998	0.2149	0.022	-0.0088	0.1993	0.0212	0.178	-18.9044	-6.7658	20.809
6	2.0128	-1.1327	0.8509	4.0607	-0.9936	2.7136	0.0062	0.0892	-0.5116	-0.0707	0.1405	0.1763	0.4819	-0.1451	-0.1591	0.2697	-0.0649	-0.0372	0.1969	-0.0204	0.2661	-29.5016	-10.5147	19.0666
7	0.5423	-0.6092	0.8201	0.8403	-1.026	2.1177	0.0089	0.013	-0.0836	-0.0314	0.0539	-0.011	0.2281	0.0942	-0.1402	0.182	0.0362	0.0069	0.1578	-0.0002	0.1471	-12.9293	-6.3516	32.2991
8	2.4911	1.3212	0.4913	2.3534	0.7361	1.0104	-0.1265	0.0567	0.1626	0.0807	0.0568	0.0337	0.0479	0.1811	0.0652	0.2393	0.0736	-0.0074	0.2385	0.0159	0.1884	-4.3587	-5.5074	46.9867
9	3.2409	1.3009	0.4984	2.3296	-0.0378	1.2596	-0.0195	-0.5549	-0.1018	0.1882	-0.2088	-0.3908	0.0179	0.3709	0.1982	0.2678	0.0823	-0.0547	0.3693	0.0419	0.2136	4.1822	-5.4436	54.0667
10	1.8026	0.2614	-0.209	1.3007	-0.9112	2.0278	-0.1511	0.0624	0.1993	0.1232	0.0382	-0.0848	-0.1139	0.0051	0.0784	0.1841	-0.0209	-0.0326	0.0894	0.011	0.1668	-16.0115	11.7423	67.8784
11	1.522	-0.5076	-1.062	2.4967	-1.1839	1.8638	0.1013	0.351	0.2546	-0.2359	-0.2769	0.0625	-0.1745	-0.1213	0.1606	0.2523	0.0201	-0.0807	0.186	-0.0126	0.3193	-23.0164	28.2625	43.3844
12	4.3255	-0.6305	0.6133	1.8084	-0.4662	1.2773	-0.2188	-0.2542	0.4896	0.3364	0.0246	-0.2482	-0.1498	-0.0425	0.1889	0.2194	0.0294	-0.0838	0.2138	-0.0359	0.2382	-28.6739	28.8608	45.308
13	3.0996	-0.3362	0.8295	1.9804	-0.5055	2.4982	0.1533	0.3331	-0.1249	-0.245	-0.0568	0.3098	0.3982	-0.0415	-0.0824	0.2315	-0.0408	-0.0269	0.1335	-0.0115	0.1679	-25.5608	-7.3809	52.6285
14	2.5475	0.024	0.4526	4.7861	-1.0936	3.9059	-0.0211	0.1218	0.2293	-0.0526	0.0413	0.2579	-0.4536	-0.0901	0.0086	0.2034	-0.0284	-0.0013	0.1578	0.0117	0.1693	-29.1251	3.887	58.3486
15	3.1094	-0.4878	1.1411	1.7659	-0.8091	2.6762	0.1277	-0.1386	-0.1486	0.0219	0.0555	0.3881	0.2161	-0.4894	-0.1419	0.2003	-0.0889	0.0255	0.2223	0.0364	0.2367	-33.2618	-6.4039	60.3346
16	0.7263	-0.8247	1.2738	3.4025	-2.1729	5.6252	-0.0723	0.1984	-0.1002	0.0259	0.1989	0.5919	-0.0406	-0.3372	-0.0759	0.1744	-0.0415	0.0058	0.2076	-0.0022	0.2759	-32.3637	0.8552	52.9185
17	0.6957	-0.5434	0.9631	0.6478	-0.6186	1.7459	0.0381	0.0338	0.1048	-0.1109	-0.0985	-0.0227	0.0677	0.0031	0.0661	0.1425	0.0219	0.023	0.1862	0.0019	0.2069	-27.3569	15.8198	38.704
18	3.5599	1.7103	-1.4654	2.0816	-0.1765	1.4276	0.1071	0.2204	0.0972	0.0741	0.0267	-0.0516	-0.1591	-0.0348	-0.0961	0.1887	0.0518	-0.0299	0.2499	0.0244	0.2032	-27.2212	17.178	33.6836
19	2.8078	1.4306	0.4915	2.7051	0.1038	1.1608	-0.2526	0.3425	0.5216	-0.3978	0.0512	0.0647	-0.2267	0.1272	0.1569	0.2256	0.0049	-0.0348	0.2462	0.0854	0.2588	-27.1706	26.6678	24.7219

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 113 )	H	1 - 113
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 114 through 141 )	H	114 - 141
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 142 through 220 )	H	142 - 220
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 32 )	L	1 - 32
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 33 through 48 )	L	33 - 48
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 49 through 75 )	L	49 - 75
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 76 through 128 )	L	76 - 128
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 174 )	L	129 - 174
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 175 through 213 )	L	175 - 213
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 1 through 113 )	A	1 - 113
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 114 through 141 )	A	114 - 141
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 142 through 220 )	A	142 - 220
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 32 )	B	1 - 32
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 33 through 48 )	B	33 - 48
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 49 through 75 )	B	49 - 75
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 76 through 90 )	B	76 - 90
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 91 through 150 )	B	91 - 150
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 151 through 174 )	B	151 - 174
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 175 through 213 )	B	175 - 213

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Yorodumi