PDB-5ff6: Cetuximab Fab in complex with L10Q meditope variant

ID or keywords:

Entry

Database: PDB / ID: 5ff6

Title

Cetuximab Fab in complex with L10Q meditope variant

Components

(Cetuximab Fab ...) x 2
L10Q meditope

Keywords

IMMUNE SYSTEM /

antibody / anti-EGFR

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

PHOSPHATE ION

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

HOMO SAPIENS (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Bzymek, K.P. / Williams, J.C.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.

History

Deposition	Dec 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Dec 13, 2017	Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ff/5ff6 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ff6	HTTPS FTP

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Related structure data

Related structure data	5etuC 5eukC 5f88C 5i2iC 5iopC 5ir1C 5itfC 5iv2C 5ivzC 5t1kC 5t1lC 5t1mC 5th2C 4gw1S 5esq C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hyq-1 5esq-2 5icz-2 5euk-1 6au5-2 5id1-1 5t1k-1 5icx-2 5i19-d 5hyq-2 4r7d-1 5id0-1 5t1l-2 5etu-2 5ivz-2 5vr9-1 6axp-2 6xul-5 5icz-1 5nyx-2 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

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

A: Cetuximab Fab light chain

B: Cetuximab Fab heavy chain

C: Cetuximab Fab light chain

D: Cetuximab Fab heavy chain

E: L10Q meditope

F: L10Q meditope

hetero molecules

98.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cetuximab Fab light chain

B: Cetuximab Fab heavy chain

E: L10Q meditope

hetero molecules

defined by author&software
48.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cetuximab Fab light chain

D: Cetuximab Fab heavy chain

F: L10Q meditope

hetero molecules

defined by author&software
49.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.080, 83.050, 212.670
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody	Cetuximab Fab light chain Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Description: commercially available / Production host: unidentified (others)
#2: Antibody	Cetuximab Fab heavy chain Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Description: commercially available / Production host: unidentified (others)

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Protein/peptide / Sugars , 2 types, 4 molecules EF

#3: Protein/peptide

L10Q meditope

Mass: 1487.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#5: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 540 molecules

#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M citric acid, 0.1 M sodium hydrogen phosphate, 0.4 M potassium hydrogen phosphate, 1.6 M sodium dihydrogen phosphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 19, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.5→33.12 Å / Num. obs: 39902 / % possible obs: 99.3 % / Redundancy: 4.8 % / R_merge(I) obs: 0.049 / Net I/σ(I): 23.5
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.185 / Mean I/σ(I) obs: 7.3 / % possible all: 92.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1

Resolution: 2.5→32.726 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 17.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2005	1996	5 %
R_work	0.1551	-	-
obs	0.1575	39902	99.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→32.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6780	0	40	532	7352

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7023
X-RAY DIFFRACTION	f_angle_d	1.18	9582
X-RAY DIFFRACTION	f_dihedral_angle_d	11.706	4184
X-RAY DIFFRACTION	f_chiral_restr	0.078	1080
X-RAY DIFFRACTION	f_plane_restr	0.004	1222

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 (%)
2.5-2.5625	0.2666	131	0.1941	2483	X-RAY DIFFRACTION	92
2.5625-2.6318	0.2419	139	0.1742	2645	X-RAY DIFFRACTION	100
2.6318-2.7092	0.2504	141	0.1794	2683	X-RAY DIFFRACTION	100
2.7092-2.7966	0.2673	142	0.1812	2696	X-RAY DIFFRACTION	100
2.7966-2.8965	0.24	142	0.178	2695	X-RAY DIFFRACTION	100
2.8965-3.0124	0.2215	141	0.1703	2688	X-RAY DIFFRACTION	100
3.0124-3.1494	0.2174	141	0.1632	2683	X-RAY DIFFRACTION	100
3.1494-3.3152	0.1825	144	0.1669	2723	X-RAY DIFFRACTION	100
3.3152-3.5227	0.2063	142	0.1504	2700	X-RAY DIFFRACTION	100
3.5227-3.7944	0.2025	144	0.1449	2736	X-RAY DIFFRACTION	100
3.7944-4.1755	0.1862	143	0.1338	2710	X-RAY DIFFRACTION	100
4.1755-4.7781	0.1437	145	0.115	2757	X-RAY DIFFRACTION	100
4.7781-6.0138	0.1716	146	0.1366	2790	X-RAY DIFFRACTION	100
6.0138-32.7291	0.183	155	0.1824	2917	X-RAY DIFFRACTION	100

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	1.8545	0.2423	0.6388	2.293	-0.7979	3.5196	0.088	-0.0121	0.0972	0.0785	0.0363	-0.0239	-0.4721	-0.0575	-0.1595	0.2538	0.0193	0.0384	0.1721	-0.0254	0.1439	24.9734	-25.6832	-15.4461
2	1.8679	0.7131	-0.7704	6.2931	-4.1416	5.9372	0.1095	-0.0684	0.2465	0.0884	0.056	0.1504	-0.2245	0.1915	-0.1629	0.1614	-0.0011	0.02	0.204	-0.0457	0.1273	25.795	-29.4694	-17.4563
3	0.1636	0.2882	-0.4861	1.5996	-2.781	4.8583	-0.1777	0.0768	0.0583	0.2317	0.0338	0.0621	-0.1331	0.1987	-0.1002	0.3673	0.0586	0.0422	0.0906	-0.0346	0.1682	24.698	-18.3622	-35.4042
4	1.6485	0.0147	0.9619	4.153	2.7259	4.352	-0.122	0.0065	-0.0631	0.0138	0.1175	0.147	0.23	0.0856	0.0167	0.1236	0.0088	0.0211	0.1499	0.0296	0.2007	28.4467	-30.9209	-53.802
5	3.2617	1.4674	4.1487	1.8285	3.1736	6.6414	-0.1549	0.0806	0.2652	-0.1235	-0.1225	0.1852	-0.2989	-0.4595	0.2924	0.1606	-0.0476	-0.0148	0.2885	-0.0347	0.2726	19.8044	-33.7641	-55.7809
6	2.0793	-0.5777	0.9117	4.2154	2.1377	3.921	0.1622	0.2884	0.0255	-0.3231	-0.2081	0.141	0.1742	0.0188	0.0247	0.1495	0.0221	0.0021	0.2249	-0.0382	0.1962	26.7397	-28.4682	-54.9543
7	5.6629	2.7387	4.1102	4.0464	2.4245	6.7939	-0.0033	-0.0419	-0.3527	-0.1615	-0.0298	-0.4452	0.2282	0.2382	0.0248	0.1749	0.0747	0.0083	0.2195	-0.0086	0.2346	38.2586	-48.2507	-20.4852
8	5.8835	-3.0811	5.0726	5.1056	-3.9166	7.0544	-0.05	-0.2446	0.0531	-0.2125	0.0196	0.1044	0.4357	-0.303	-0.0225	0.1712	0.0077	-0.0165	0.1476	-0.0124	0.1777	27.1407	-44.1063	-17.6624
9	6.6461	-0.8839	1.4505	2.959	0.0684	3.5158	-0.0211	-0.5173	-0.2179	0.0838	0.0557	0.0547	0.812	-0.0515	-0.0232	0.3704	-0.0806	0.021	0.2098	0.0379	0.181	30.2966	-52.3551	-10.9235
10	6.3478	1.4168	4.6998	3.1808	1.3122	6.824	0.2878	-0.189	-0.4717	0.2177	0.0063	0.0983	0.8911	-0.1093	-0.374	0.3643	-0.0135	-0.0201	0.1633	-0.0361	0.2108	32.6249	-53.131	-20.3775
11	0.2139	0.2085	-0.7143	0.0358	0.1161	4.656	0.0376	-0.0128	-0.0913	0.1001	0.0094	-0.055	0.2318	-0.1477	-0.0366	0.1708	0.0417	0.0114	0.1506	0.01	0.1815	33.8496	-42.6517	-24.7576
12	3.5158	0.9231	0.977	2.4513	2.9141	3.4687	-0.1851	0.0547	0.6068	-1.1366	0.0735	0.4184	-0.1593	0.2001	-0.016	0.1518	-0.0156	-0.0551	0.2416	0.0157	0.2657	37.1352	-31.1493	-53.0062
13	8.9722	7.8543	-3.0244	8.9752	-3.0324	1.1482	0.0192	-0.7561	-0.2367	0.009	-0.2324	-0.4127	-0.1119	0.0024	0.1765	0.1445	-0.0069	-0.0176	0.2582	-0.055	0.224	38.9032	-39.8811	-40.1516
14	0.1431	-0.377	0.2009	1.8358	-0.1474	1.4088	-0.1399	-0.0591	0.0947	-0.0284	0.0037	0.1789	0.0042	-0.0056	0.1466	0.1408	0.0063	0.0091	0.1823	-0.044	0.2038	35.0033	-33.7441	-45.2315
15	4.4888	4.4483	-4.4551	5.949	-7.0326	9.2302	0.3566	-0.4679	-0.3474	-0.161	-0.5816	-0.1342	0.0764	0.8616	0.2567	0.1481	0.0761	0.0323	0.2379	0.0411	0.2768	45.0359	-37.5856	-45.4301
16	5.9306	2.3755	-2.9337	3.3835	-2.1414	4.8872	-0.1361	-0.2951	-0.2811	0.1256	-0.5882	-0.3526	0.2834	0.715	0.498	0.1979	0.0296	-0.0041	0.1219	-0.072	0.2595	40.851	-41.4482	-46.5187
17	3.2169	0.0484	0.4853	2.1334	0.9372	5.1177	0.2228	0.0236	-0.1418	-0.0786	0.0556	-0.2262	0.2284	-0.0095	-0.2744	0.2047	0.0362	0.0225	0.1658	0.001	0.152	9.9188	-14.65	-14.6571
18	0.8712	0.2516	-1.512	3.4301	-0.684	2.6067	-0.0761	-0.1895	-0.2317	-0.0867	0.1784	0.1744	0.4624	-0.3355	-0.1077	0.2489	-0.0057	-0.028	0.1757	0.0435	0.2096	1.108	-15.6924	-12.9788
19	1.536	-0.334	0.2297	4.3215	3.6413	5.6085	0.0379	-0.0976	-0.1162	0.0388	-0.0071	0.0933	0.0746	0.0803	-0.0042	0.2367	0.027	-0.0116	0.1961	0.0198	0.117	5.7528	-10.8797	-15.4628
20	0.3885	0.7716	0.555	6.6029	5.1442	4.032	-0.0885	-0.0675	0.2541	0.7912	0.1374	-0.0328	0.6873	0.0804	0.0063	0.2697	0.0239	0.0005	0.1851	-0.0213	0.2229	6.1611	-21.2847	-35.3805
21	1.796	-0.1104	-1.3917	3.6129	0.6882	1.6224	0.272	0.5214	0.1018	-0.3019	-0.1768	-0.2836	-0.1846	-0.1999	-0.1168	0.1421	-0.0375	-0.0652	0.3009	0.0219	0.1975	-2.5187	0.4113	-55.5011
22	1.3689	1.0013	-1.3511	8.5799	-6.1518	4.7646	-0.295	-0.1733	-0.1314	-0.0458	0.1911	-0.2868	0.0602	0.1139	0.1581	0.142	-0.0445	-0.0159	0.1506	-0.0434	0.2058	7.0599	-10.2926	-48.9275
23	2.212	0.5642	-1.4294	1.7572	-2.0787	3.3309	-0.1224	0.4545	0.0486	-0.0128	0.1932	-0.1677	0.3138	-0.4688	-0.0405	0.1228	-0.0727	0.0241	0.2236	-0.0247	0.208	12.0165	-3.7701	-53.1229
24	1.2914	0.7943	-0.6541	3.5607	-2.8716	4.2051	-0.1071	0.2056	-0.0617	-0.1996	0.072	-0.0359	0.1233	-0.1972	-0.0091	0.1072	-0.001	0.0178	0.2353	-0.0135	0.1625	5.2541	-8.5515	-53.3574
25	8.5829	3.8902	-3.7627	6.9597	-3.947	9.1211	-0.5316	0.2564	0.0679	-0.5658	0.3221	0.0992	-0.5012	-0.2478	0.1976	0.2989	0.0601	-0.0402	0.1752	-0.0026	0.2437	-3.1298	10.2643	-22.4685
26	2.1809	0.7714	-1.0963	1.2017	0.0325	4.1404	0.0465	-0.1153	0.2483	0.0238	0.0897	0.033	-0.2661	-0.0817	-0.1297	0.2705	0.0404	0.0002	0.1637	0.0156	0.1977	-0.7054	7.1811	-11.7279
27	0.4833	-0.0425	0.4014	1.7511	-1.3092	3.0038	-0.0544	-0.0371	0.044	0.1019	-0.0103	-0.0759	-0.5446	-0.3448	0.0746	0.0489	0.0046	0.0034	0.1867	-0.0296	0.1756	-2.493	4.0873	-33.7087
28	2.0636	1.6178	0.9659	3.5992	0.8387	1.7804	0.0503	-0.0858	0.0841	0.0664	-0.1293	0.1492	-0.0497	-0.1763	0.0544	0.0996	0.0117	0.0317	0.1917	0.0138	0.1613	-6.6933	-0.7698	-42.7986
29	8.1959	-3.0677	0.3199	2.964	0.303	6.4601	0.0687	-0.2302	-0.0154	-0.9386	-0.3743	0.4032	-0.7128	-0.8327	0.2544	0.279	0.0237	-0.0047	0.2495	-0.0829	0.2916	23.44	-35.0605	-30.9042
30	4.8036	-2.6583	-2.0722	4.2479	3.8345	3.5303	0.2356	0.2147	0.1615	-1.0266	0.0588	-0.4536	-0.586	0.6156	-0.3224	0.3128	0.0216	0.0434	0.2837	0.0656	0.2923	7.8562	-4.5494	-28.5088

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1:75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76:101 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 102:113 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 114:150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151:163 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 164:213 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1:33 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34:51 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 52:72 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73:90 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91:130 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 131:151 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 152:163 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 164:194 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 195:209 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 210:220)
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1:38 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 39:75 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 76:102 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 103:113 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 114:128 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 129:150 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 151:163 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 164:213 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 1:17 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 18:105 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 106:140 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 141:220 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 1:12 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 1:12 )

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