PDB-6ugv: Crystal structure of the Fab fragment of anti-TNFa antibody infli...

ID or keywords:

Entry

Database: PDB / ID: 6ugv

Title

Crystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a I-centered orthorhombic crystal form, Lot C

Components

Infliximab Fab Heavy Chain
Infliximab Fab Light Chain

Keywords

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

Function / homology

Function and homology information

immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Conlan, H.D.

Citation

Journal: BioDrugs / Year: 2020
Title: Crystal Structures of PF-06438179/GP1111, an Infliximab Biosimilar.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Zou, Q. / Conlon, H.D.

History

Deposition	Sep 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Oct 11, 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 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ugv.cif.gz	356.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6ugv.ent.gz	289 KB	Display	PDB format
PDBx/mmJSON format	6ugv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ugv_validation.pdf.gz	460.8 KB	Display	wwPDB validaton report
Full document	6ugv_full_validation.pdf.gz	463.2 KB	Display
Data in XML	6ugv_validation.xml.gz	37.7 KB	Display
Data in CIF	6ugv_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/6ugv ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ugv	HTTPS FTP

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Related structure data

Related structure data	6ugsC 6ugtC 6uguC 6ugwC 6ugxC 6ugyC 4g3yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5xrq-1 3ejy-4 6ele-1 4yhm-d 4kkl-3 5f6i-d 6df2-1 5t78-1 1ngy-d 6ev1-6 5f6h-4 4r7d-2 6mh2-2 5jw5-2 4kaq-d 6ell-1 6wgb-1 4r90-d 4ygv-1 4kk5-3 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

Related structure data

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: Infliximab Fab Heavy Chain

L: Infliximab Fab Light Chain

A: Infliximab Fab Heavy Chain

B: Infliximab Fab Light Chain

hetero molecules

96.1 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 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
48.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.660, 93.300, 315.660
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-448- HOH
2	1	H-457- HOH
3	1	A-542- 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.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: A8K008
#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.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: Q6P5S8
#3: Chemical	ChemComp-MRY / MESO-ERYTHRITOL Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.49 Å³/Da / Density % sol: 64.76 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mg/mL PF06438179 Fab lot A against 2.16 M sodium malonate, 4% pentaerythritol ethoxylate, crystal tracking ID 267670e4, unique puck ID sar8-9

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 52789 / % possible obs: 99.9 % / Redundancy: 6.19 % / B_iso Wilson estimate: 31.46 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.137 / Χ²: 0.946 / Net I/σ(I): 12.66

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
2.4-2.46	6.282	0.79	2.68	3860	0.791	0.861	99.9
2.46-2.53	6.276	0.669	3.13	3740	0.851	0.73	99.9
2.53-2.6	6.292	0.579	3.62	3684	0.868	0.632	100
2.6-2.68	6.281	0.447	4.57	3506	0.912	0.488	99.9
2.68-2.77	6.288	0.363	5.53	3479	0.945	0.395	100
2.77-2.87	6.277	0.302	6.41	3336	0.959	0.33	100
2.87-2.98	6.265	0.24	7.96	3223	0.972	0.262	99.9
2.98-3.1	6.26	0.184	10.03	3154	0.982	0.201	99.9
3.1-3.24	6.246	0.143	12.27	2968	0.989	0.155	99.9
3.24-3.39	6.216	0.115	14.61	2841	0.993	0.126	99.9
3.39-3.58	6.178	0.099	16.65	2723	0.994	0.109	99.8
3.58-3.79	6.17	0.087	18.58	2595	0.995	0.095	100
3.79-4.06	6.149	0.073	21.28	2438	0.996	0.08	99.9
4.06-4.38	6.101	0.061	24.88	2257	0.997	0.067	99.8
4.38-4.8	6.056	0.055	26.98	2096	0.997	0.06	99.9
4.8-5.37	6.075	0.055	26.47	1919	0.997	0.061	99.9
5.37-6.2	6.039	0.061	24.11	1702	0.997	0.066	99.9
6.2-7.59	5.957	0.058	24.6	1450	0.997	0.064	100
7.59-10.73	5.761	0.044	31.03	1150	0.998	0.048	100
10.73-50	5.1	0.044	29.42	668	0.998	0.049	97.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4G3Y

4g3y

Resolution: 2.4→50 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.41

	R_factor	Num. reflection	% reflection
R_free	0.2099	2620	4.96 %
R_work	0.1527	-	-
obs	0.1555	52775	99.89 %

Solvent computation

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

Displacement parameters

B_iso max: 127.66 Å² / B_iso mean: 34.8659 Å² / B_iso min: 13.4 Å²

Refinement step

Cycle: final / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6570	0	28	615	7213
B_iso mean	-	-	87.42	41.34	-
Num. residues	-	-	-	-	868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6786
X-RAY DIFFRACTION	f_angle_d	0.848	9242
X-RAY DIFFRACTION	f_chiral_restr	0.052	1037
X-RAY DIFFRACTION	f_plane_restr	0.004	1185
X-RAY DIFFRACTION	f_dihedral_angle_d	13.406	4029

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
2.4001-2.4437	0.2538	134	0.21	2600
2.4437-2.4907	0.2878	135	0.2238	2585
2.4907-2.5416	0.308	142	0.2163	2624
2.5416-2.5968	0.2466	117	0.2048	2627
2.5968-2.6572	0.288	143	0.1907	2604
2.6572-2.7237	0.2585	131	0.1865	2597
2.7237-2.7973	0.2266	132	0.1823	2637
2.7973-2.8796	0.2326	123	0.1757	2622
2.8796-2.9726	0.2386	147	0.1827	2598
2.9726-3.0788	0.2309	161	0.1755	2600
3.0788-3.202	0.2193	171	0.1648	2596
3.202-3.3477	0.1824	156	0.147	2640
3.3477-3.5241	0.2285	137	0.1394	2618
3.5241-3.7449	0.2066	128	0.1346	2645
3.7449-4.0339	0.2034	111	0.1255	2672
4.0339-4.4395	0.1538	117	0.106	2685
4.4395-5.0812	0.1442	135	0.1037	2679
5.0812-6.3992	0.1571	122	0.1472	2724
6.3992-50	0.2079	178	0.1683	2802

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	2.9733	1.162	1.554	2.6384	1.156	3.1706	-0.0102	0.1377	0.0343	-0.0805	0.0029	-0.1002	-0.1297	0.124	0.0032	0.18	-0.0273	-0.004	0.1956	0.0154	0.1456	-10.8685	6.2367	11.0095
2	1.2921	-1.118	0.9468	1.958	-0.5383	1.6818	-0.2409	-0.031	0.224	0.2973	0.0835	-0.5078	0.0003	0.275	0.1091	0.2242	-0.0089	-0.0492	0.2438	0.0134	0.3496	5.6897	-1.2322	35.7014
3	1.8255	-0.1376	0.3194	6.9667	-1.641	1.6717	-0.1787	0.1172	0.2892	-0.1384	0.0532	-0.5122	-0.147	0.1716	0.1246	0.2296	-0.0511	-0.0351	0.2084	0.0218	0.2589	6.0124	-6.5476	33.4543
4	3.1211	-3.3997	3.9164	4.5208	-5.9825	8.3404	-0.0234	-0.3726	-0.3393	0.3013	0.0834	0.1331	0.0667	-0.3587	-0.0681	0.2378	-0.0539	-0.005	0.32	0.0587	0.2353	-27.6965	-4.7328	30.3306
5	2.8227	-1.4722	-0.0143	4.8951	-1.1929	4.0067	0.0457	-0.037	-0.4376	-0.1082	0.0118	0.1842	0.3019	-0.1604	-0.0638	0.1805	-0.0666	-0.0418	0.2386	-0.0089	0.1919	-26.7211	-7.2184	20.0717
6	0.6525	-0.99	0.9963	1.2215	-1.1364	2.4631	-0.1266	-0.0643	-0.0781	0.0442	0.2086	0.0139	0.0041	-0.1489	-0.1577	0.1923	-0.0231	-0.0065	0.1481	0.0002	0.2033	-12.8126	-6.1	32.3783
7	4.8739	1.7577	1.3035	2.9096	0.7324	1.9007	-0.1432	-0.1823	0.1534	0.3698	0.1773	-0.1744	-0.2594	0.0618	-0.0017	0.2963	0.0521	-0.0681	0.2093	-0.014	0.2108	-4.2965	-5.5196	47.1288
8	8.2361	3.1317	0.9726	3.4686	0.1287	1.8827	-0.0291	-0.9987	0.0642	0.5499	-0.1173	-0.4345	-0.1804	0.2205	0.1342	0.4294	0.0808	-0.1438	0.3678	-0.0509	0.2528	4.1586	-5.3785	54.1215
9	1.8414	0.2555	-0.1352	2.8137	-1.3239	3.8099	-0.0623	-0.051	0.2372	0.2466	0.0213	-0.0681	-0.0263	0.0434	0.0253	0.19	-0.0309	-0.0123	0.17	-0.0175	0.2055	-15.6555	12.8621	66.4616
10	3.9415	1.2082	-1.9491	3.5848	-1.2133	2.2818	0.4665	0.8018	0.6584	-0.139	-0.323	-0.0232	0.0612	0.1277	-0.2086	0.2315	0.0933	0.034	0.2592	-0.0094	0.3523	-33.4358	31.6475	35.1737
11	7.9696	-0.802	1.6472	2.2044	-0.8876	2.3974	0.0342	-0.2852	0.5468	0.2261	-0.1096	-0.2207	-0.2822	0.1186	0.0527	0.2112	-0.0472	0.0023	0.191	-0.021	0.2286	-28.1952	28.7542	45.1591
12	3.7518	-1.4416	1.5286	2.4529	-0.4625	4.1456	0.0686	0.0287	-0.0989	0.0319	0.0118	0.4216	0.2503	-0.2864	-0.075	0.2671	-0.0994	0.0069	0.1919	0.0212	0.2369	-29.1599	-4.1825	56.6212
13	1.0239	-0.8871	0.9953	1.0181	-0.7707	2.4111	0.2051	-0.0303	-0.0028	-0.0566	-0.0716	0.1859	0.1592	-0.0451	-0.1787	0.1592	-0.0343	0.0231	0.1798	0.0047	0.2171	-28.4298	10.1346	46.4941
14	4.0151	2.4606	-0.5366	3.6272	-0.9825	1.3043	0.1596	0.4389	0.0004	-0.0807	-0.0202	-0.0906	-0.0449	0.1153	-0.0859	0.2081	0.0593	-0.0015	0.2887	0.0157	0.1828	-27.7892	18.0597	31.8898
15	4.73	2.7326	0.5644	5.9936	-0.0947	2.7104	-0.219	0.7358	0.5164	-0.6319	0.1417	-0.0219	-0.325	0.3529	0.054	0.2954	0.0284	0.0198	0.3825	0.1149	0.2493	-26.986	26.839	24.5625

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 18 )	L	1 - 18
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 19 through 75 )	L	19 - 75
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 76 through 128 )	L	76 - 128
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 129 through 174 )	L	129 - 174
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 175 through 213 )	L	175 - 213
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 126 )	A	1 - 126
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 127 through 141 )	A	127 - 141
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 142 through 220 )	A	142 - 220
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 75 )	B	1 - 75
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 76 through 128 )	B	76 - 128
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 129 through 174 )	B	129 - 174
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 175 through 213 )	B	175 - 213

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