PDB-6ugs: Crystal structure of the Fab fragment of PF06438179/GP1111 an inf...

ID or keywords:

Entry

Database: PDB / ID: 6ugs

Title

Crystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a C-centered orthorhombic crystal form, Lot A

Components

Infliximab (Remicade) Fab Heavy Chain
Infliximab (Remicade) Fab Light Chain

Keywords

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

Function / homology

Function and homology information

extracellular region / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

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

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 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ugs.cif.gz	362.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ugs_validation.pdf.gz	250.9 KB	Display	wwPDB validaton report
Full document	6ugs_full_validation.pdf.gz	250.9 KB	Display
Data in XML	6ugs_validation.xml.gz	1.1 KB	Display
Data in CIF	6ugs_validation.cif.gz	14.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/6ugs ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ugs	HTTPS FTP

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Related structure data

Related structure data	6ugtC 6uguC 6ugvC 6ugwC 6ugxC 6ugyC 4g3yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vh3-2 6btj-2 3i9g-d 5it2-d 3qpq-4 6ugu-1 6ugu-2 1ghf-d 6w7y-2 1hil-2 5t0y-1 1d5i-d 6ev2-2 4m43-d 4kjw-2 1a4k-1 4uik-d 3dgg-2 3eyf-1 6a0x-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 (Remicade) Fab Heavy Chain

L: Infliximab (Remicade) Fab Light Chain

A: Infliximab (Remicade) Fab Heavy Chain

B: Infliximab (Remicade) Fab Light Chain

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

1

H: Infliximab (Remicade) Fab Heavy Chain

L: Infliximab (Remicade) Fab Light Chain

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

2

A: Infliximab (Remicade) Fab Heavy Chain

B: Infliximab (Remicade) Fab Light Chain

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

Unit cell

Length a, b, c (Å)	87.210, 139.090, 195.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Antibody	Infliximab (Remicade) 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 (Remicade) 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1047 / 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: 3.1 Å³/Da / Density % sol: 60 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mg/mL PF06438179 Fab lot A against 19.5% PEG 10000, 0.1 M HEPES pH 7.8, supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267659h4, unique puck ID lqb9-8

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 19, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 86561 / % possible obs: 99.9 % / Redundancy: 6.191 % / B_iso Wilson estimate: 23.64 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.084 / Χ²: 0.992 / Net I/σ(I): 15.61

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
1.95-2	6.259	0.491	3.53	6356	0.921	0.536	100
2-2.06	6.276	0.389	4.45	6182	0.944	0.424	100
2.06-2.12	6.254	0.328	5.33	6015	0.959	0.358	100
2.12-2.18	6.25	0.271	6.47	5852	0.97	0.295	100
2.18-2.25	6.282	0.224	7.64	5665	0.975	0.245	99.9
2.25-2.33	6.281	0.197	8.63	5485	0.98	0.215	99.9
2.33-2.42	6.278	0.178	9.43	5328	0.984	0.195	99.9
2.42-2.52	6.269	0.147	11.32	5082	0.988	0.16	99.9
2.52-2.63	6.27	0.12	13.5	4916	0.992	0.13	99.9
2.63-2.76	6.242	0.099	15.64	4700	0.995	0.108	100
2.76-2.91	6.221	0.084	18.7	4484	0.996	0.091	99.9
2.91-3.08	6.199	0.07	22.16	4223	0.997	0.076	100
3.08-3.3	6.131	0.058	26.33	3999	0.997	0.063	100
3.3-3.56	6.076	0.05	29.93	3714	0.998	0.055	99.9
3.56-3.9	6.045	0.046	31.92	3450	0.998	0.05	99.9
3.9-4.36	5.982	0.041	34.37	3126	0.998	0.045	99.8
4.36-5.03	5.982	0.038	36.12	2743	0.999	0.041	99.8
5.03-6.17	5.991	0.037	35.18	2376	0.999	0.041	99.9
6.17-8.72	5.836	0.037	34.49	1851	0.999	0.04	99.7
8.72-50	5.384	0.036	34.75	1014	0.998	0.04	94.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_2229	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4G3Y

4g3y

Resolution: 1.95→50 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.06

	R_factor	Num. reflection	% reflection
R_free	0.198	4246	4.91 %
R_work	0.1588	-	-
obs	0.1607	86525	99.83 %

Solvent computation

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

Displacement parameters

B_iso max: 91.65 Å² / B_iso mean: 31.8318 Å² / B_iso min: 13.69 Å²

Refinement step

Cycle: final / Resolution: 1.95→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6506	0	0	1048	7554
B_iso mean	-	-	-	39.88	-
Num. residues	-	-	-	-	864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6688
X-RAY DIFFRACTION	f_angle_d	0.789	9124
X-RAY DIFFRACTION	f_chiral_restr	0.054	1029
X-RAY DIFFRACTION	f_plane_restr	0.005	1170
X-RAY DIFFRACTION	f_dihedral_angle_d	13.115	3972

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.95-1.9722	0.2769	129	0.2273	2687	100
1.9722-1.9954	0.2799	149	0.2013	2743	100
1.9954-2.0197	0.2711	107	0.1995	2737	100
2.0197-2.0453	0.2472	161	0.1971	2700	100
2.0453-2.0722	0.2561	164	0.1807	2670	100
2.0722-2.1006	0.2137	176	0.1837	2731	100
2.1006-2.1306	0.225	137	0.1794	2680	100
2.1306-2.1624	0.2361	152	0.1704	2741	100
2.1624-2.1962	0.2104	175	0.169	2671	100
2.1962-2.2322	0.2197	153	0.1655	2740	100
2.2322-2.2707	0.2081	132	0.1657	2697	100
2.2707-2.312	0.1967	138	0.1647	2746	100
2.312-2.3564	0.2329	118	0.1659	2791	100
2.3564-2.4045	0.2363	125	0.1725	2718	100
2.4045-2.4568	0.1908	128	0.168	2718	100
2.4568-2.5139	0.2068	134	0.1665	2748	100
2.5139-2.5768	0.2096	132	0.1655	2765	100
2.5768-2.6465	0.2046	144	0.1633	2748	100
2.6465-2.7243	0.2412	135	0.1658	2738	100
2.7243-2.8123	0.1968	133	0.1636	2728	100
2.8123-2.9128	0.1949	148	0.164	2745	100
2.9128-3.0294	0.2142	142	0.1705	2750	100
3.0294-3.1672	0.2154	149	0.1681	2739	100
3.1672-3.3342	0.2058	152	0.1625	2727	100
3.3342-3.543	0.1814	129	0.1591	2795	100
3.543-3.8164	0.1761	134	0.1543	2772	100
3.8164-4.2003	0.1783	145	0.1372	2773	100
4.2003-4.8076	0.1316	140	0.1136	2813	100
4.8076-6.0551	0.1449	140	0.1309	2810	100
6.0551-50	0.2113	145	0.1624	2858	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	1.5809	-0.1062	-0.5634	2.4695	1.5265	2.8155	-0.0609	-0.0629	0.0588	-0.0009	0.0247	0.2724	-0.0685	-0.2182	0.02	0.1449	0.0637	-0.0119	0.18	0.031	0.2061	-32.4093	-16.695	14.7361
2	0.3701	-0.1176	0.4354	2.5815	-0.3014	0.4414	-0.1035	-0.0375	0.0716	0.1449	0.1734	0.22	0.0639	-0.0222	-0.0258	0.1795	0.0758	0.0317	0.218	0.0274	0.1991	-29.6859	-22.0507	20.0956
3	2.6889	0.6805	-1.0507	2.8959	-0.4325	4.7716	0.2638	0.1224	-0.2256	0.0355	-0.1251	-0.0494	0.2936	-0.2677	-0.125	0.2452	0.0321	-0.0886	0.189	-0.0176	0.2438	-21.2069	-51.9178	25.814
4	4.1587	-1.0242	1.1257	3.1447	1.1238	0.9479	-0.144	-0.3484	-0.234	0.7021	0.0634	0.022	-0.1579	-0.2577	0.0834	0.2687	0.1057	-0.0023	0.222	-0.0267	0.203	-12.8898	-19.0941	35.2677
5	1.4158	-0.2428	0.3437	3.0347	-0.5913	1.2955	-0.2143	-0.3851	0.0107	0.6458	0.2295	0.0897	-0.1147	-0.1305	-0.0158	0.3544	0.1943	0.0021	0.3347	-0.0108	0.2151	-21.0003	-12.0111	35.5492
6	1.4158	-0.2296	-0.4451	2.3125	-1.2044	3.0152	-0.3528	-0.4849	-0.055	0.5552	0.3327	0.0852	0.0468	-0.0911	0.0043	0.3123	0.1745	0.0272	0.3155	0.0307	0.2131	-20.6959	-15.7333	31.9725
7	2.9939	-1.9999	-0.0221	5.4809	-0.0784	3.3659	0.0185	0.05	0.3118	-0.2882	-0.0468	-0.2841	-0.296	-0.1983	0.0413	0.1953	-0.0114	-0.025	0.1397	0.0094	0.143	-11.373	-33.8219	41.9924
8	2.8979	0.1668	0.6596	2.1251	2.2624	5.4527	0.3737	0.3654	-0.6187	-0.298	-0.4163	0.1615	0.4898	-0.3551	0.0165	0.4275	0.129	-0.1133	0.2273	-0.0807	0.326	-10.4902	-55.9555	21.9326
9	1.393	-1.8236	-2.8167	4.6435	5.0938	6.6865	0.2842	0.088	0.1299	-0.3899	-0.1667	-0.0889	-0.2631	-0.0319	-0.093	0.2423	0.0888	-0.0226	0.1676	0.0157	0.1667	-6.045	-43.8178	29.4456
10	7.1511	-4.048	-2.6622	2.2854	1.5276	1.0102	0.5992	0.4128	0.439	-0.2941	-0.3674	-0.1642	-0.3166	-0.246	-0.2268	0.3457	0.1122	0.0069	0.239	0.0188	0.2691	-2.0058	-43.8767	20.9448
11	9.0588	1.0131	-4.1264	3.7892	2.5904	4.416	-0.012	0.0478	0.0126	-0.1261	-0.244	0.0949	-0.4771	-0.7316	0.1329	0.271	0.0258	-0.0263	0.2223	-0.025	0.1953	-17.0007	-38.18	38.3725
12	3.0595	-1.6542	-1.2433	4.4674	4.3395	6.3836	0.2611	0.2507	-0.1699	-0.2609	-0.0803	-0.1769	0.1035	0.0807	-0.2086	0.25	0.0685	0.0021	0.1797	0.0044	0.2313	-1.539	-51.5037	24.6775
13	0.8988	-0.0807	0.2521	1.9826	-0.8522	2.8017	-0.0359	0.0054	-0.0743	-0.0132	0.0346	-0.2657	0.1212	0.3534	0.0099	0.1477	0.0734	-0.0205	0.2213	-0.0446	0.2132	29.9648	-52.6664	15.4514
14	1.8245	-1.0013	0.1687	3.9847	0.8821	3.088	-0.0802	-0.0421	0.4108	0.1225	0.1141	-0.2952	-0.4098	0.1477	-0.0727	0.1926	-0.0088	-0.053	0.1968	-0.029	0.2855	19.7332	-18.0749	21.9194
15	1.82	-0.6601	-0.4059	2.4479	0.4917	1.1097	-0.1616	-0.2414	-0.0124	0.4161	0.1706	-0.1262	0.0743	0.1842	-0.0016	0.3146	0.1409	-0.033	0.2647	-0.0123	0.1947	17.7985	-54.6115	35.1088
16	0.5106	-1.2454	-0.9849	3.2497	2.0495	1.0886	-0.1489	-0.1482	0.0062	0.3192	0.2818	-0.1291	0.1852	0.3172	-0.1185	0.2484	0.1013	-0.0538	0.2353	-0.0371	0.213	16.9198	-47.4393	34.1956
17	4.471	-1.1685	-0.7412	5.3252	-2.997	8.4344	0.2573	0.3334	0.7216	-0.1794	-0.1217	-0.2463	-1.0913	-0.0343	-0.1513	0.2657	0.0724	-0.0012	0.1799	0.0143	0.303	8.2308	-12.9035	20.7891
18	2.4527	-2.5353	2.7393	6.1725	-5.1353	4.5667	0.1084	-0.0149	-0.0783	-0.146	0.0144	0.1269	0.0689	-0.0963	-0.1073	0.196	0.07	-0.0169	0.1655	-0.0556	0.1884	4.5519	-24.3938	28.9087
19	3.5484	-2.3682	1.7516	1.6982	-1.6045	3.304	0.1555	0.3771	-0.1219	-0.0847	-0.2113	0.1254	0.1084	0.4288	-0.0162	0.2078	0.0313	-0.0163	0.1328	-0.0226	0.2175	7.3913	-26.8743	28.5461
20	2.7435	-1.5152	0.7943	4.7981	-4.4558	6.3728	0.0993	0.2287	0.1907	0.0725	0.0803	0.1402	-0.3882	-0.3057	-0.1861	0.1721	0.0421	-0.0457	0.1734	-0.0304	0.2219	-0.361	-17.0248	24.1162

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 93 )	H	1 - 93
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 94 through 126 )	H	94 - 126
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 127 through 222 )	H	127 - 222
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 102 )	L	76 - 102
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 103 through 113 )	L	103 - 113
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 114 through 128 )	L	114 - 128
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 129 through 150 )	L	129 - 150
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 151 through 163 )	L	151 - 163
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 164 through 174 )	L	164 - 174
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 175 through 214 )	L	175 - 214
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1 through 113 )	A	1 - 113
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 114 through 222 )	A	114 - 222
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1 through 75 )	B	1 - 75
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 76 through 113 )	B	76 - 113
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 114 through 128 )	B	114 - 128
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 129 through 150 )	B	129 - 150
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 151 through 174 )	B	151 - 174
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 175 through 214 )	B	175 - 214

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