PDB-5i2i: Structure of cetuximab Fab with cyclic F3Q variant of the meditope

ID or keywords:

Entry

Database: PDB / ID: 5i2i

Title

Structure of cetuximab Fab with cyclic F3Q variant of the meditope

Components

Cetuximab Fab heavy chain
Cetuximab Fab light chain
Meditope

Keywords

IMMUNE SYSTEM / antibody

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: 2.551 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	Feb 8, 2016	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	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5i2i.cif.gz	355.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5i2i.ent.gz	291.6 KB	Display	PDB format
PDBx/mmJSON format	5i2i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5i2i_validation.pdf.gz	471.9 KB	Display	wwPDB validaton report
Full document	5i2i_full_validation.pdf.gz	478.4 KB	Display
Data in XML	5i2i_validation.xml.gz	34.8 KB	Display
Data in CIF	5i2i_validation.cif.gz	50 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i2/5i2i ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i2i	HTTPS FTP

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Related structure data

Related structure data	5etuC 5eukC 5f88C 5ff6C 5iopC 5ir1C 5itfC 5iv2C 5ivzC 5t1kC 5t1lC 5t1mC 5th2C 4gw1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6azk-1 6azk-2 5icz-1 5hyq-1 1c5d-3 4gw1-2 5hpm-2 5euk-1 5id1-1 5ir1-2 6azl-2 6azl-1 1d5b-2 5t1m-2 4kjp-3 5etu-2 4r7d-1 2q76-2 5t1l-2 5x4g-d 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

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

A: Cetuximab Fab light chain

B: Cetuximab Fab heavy chain

C: Cetuximab Fab light chain

D: Cetuximab Fab heavy chain

E: Meditope

F: Meditope

hetero molecules

97.1 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: Meditope

hetero molecules

defined by author&software
48.6 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: Meditope

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.970, 82.500, 211.880
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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 / 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 / Production host: unidentified (others)
#3: Protein/peptide	Meditope Mass: 1361.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.89 Å³/Da / Density % sol: 57.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.5 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic

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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: Jul 11, 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: 2.55→35 Å / Num. obs: 37040 / % possible obs: 99 % / Redundancy: 4 % / Net I/σ(I): 17.8
Reflection shell	Resolution: 2.55→2.62 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.68 / % possible all: 90.1

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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: 2.551→32.948 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2048	1852	5 %
R_work	0.1596	-	-
obs	0.1618	37030	99.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.551→32.948 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6750	0	20	333	7103

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6958
X-RAY DIFFRACTION	f_angle_d	0.875	9489
X-RAY DIFFRACTION	f_dihedral_angle_d	14.559	2505
X-RAY DIFFRACTION	f_chiral_restr	0.053	1069
X-RAY DIFFRACTION	f_plane_restr	0.005	1216

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 (%)
2.5514-2.6204	0.2722	126	0.1924	2393	X-RAY DIFFRACTION	90
2.6204-2.6975	0.2526	142	0.1933	2701	X-RAY DIFFRACTION	100
2.6975-2.7845	0.27	142	0.1912	2699	X-RAY DIFFRACTION	100
2.7845-2.8839	0.2436	141	0.1896	2677	X-RAY DIFFRACTION	100
2.8839-2.9993	0.2489	141	0.1915	2695	X-RAY DIFFRACTION	100
2.9993-3.1357	0.2612	142	0.1861	2686	X-RAY DIFFRACTION	100
3.1357-3.3009	0.2107	143	0.1855	2726	X-RAY DIFFRACTION	100
3.3009-3.5075	0.2526	142	0.1553	2691	X-RAY DIFFRACTION	100
3.5075-3.778	0.1818	144	0.1471	2734	X-RAY DIFFRACTION	100
3.778-4.1575	0.1717	143	0.1329	2721	X-RAY DIFFRACTION	100
4.1575-4.7576	0.1381	145	0.1121	2752	X-RAY DIFFRACTION	100
4.7576-5.9881	0.1632	146	0.1331	2784	X-RAY DIFFRACTION	100
5.9881-32.9509	0.211	155	0.1897	2919	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	1.4136	0.349	-0.717	2.2043	0.7386	3.1268	0.1495	-0.0934	-0.2348	0.3348	0.1516	-0.1263	0.9654	0.148	-0.3197	0.4995	0.0684	-0.1116	0.2873	0.0348	0.2353	7.1882	25.4033	-15.3847
2	0.5877	-0.0584	-0.2007	1.0547	1.7623	3.067	0.0745	0.0646	-0.0075	0.1642	0.0898	-0.0355	0.3286	0.0204	-0.1667	0.1277	0.0025	-0.0073	0.2177	0.0444	0.2358	5.3163	28.3802	-38.1626
3	1.3327	-0.0797	-0.8004	2.9445	-1.7332	3.4503	0.0756	0.2119	0.0113	-0.1786	-0.0463	-0.1277	-0.0999	0.0121	-0.0656	0.1466	-0.033	-0.0177	0.2676	-0.0109	0.2432	6.7176	29.1199	-55.2264
4	4.3795	1.154	-3.0291	1.8219	-1.9543	7.6514	-0.4206	0.5148	0.4952	-0.4853	0.4638	0.0716	-0.05	-0.4553	-0.051	0.2791	0.07	-0.0178	0.252	0.0806	0.307	-2.7782	49.9543	-26.4246
5	0.377	-0.3034	0.9765	0.7594	0.8617	4.8728	-0.037	0.0032	0.0941	0.0518	0.0417	0.0044	-0.3626	-0.1357	-0.0191	0.2034	0.0114	0.0233	0.1723	0.0306	0.2175	-0.8357	46.7293	-18.8883
6	3.2952	3.0148	1.201	6.5943	1.0997	0.9699	-0.1513	0.074	-0.1704	-0.1881	0.0978	-0.133	-0.0222	0.0732	0.0278	0.1113	0.0139	0.0047	0.2297	0.0539	0.2192	-4.3234	33.8801	-46.5131
7	4.7979	4.2643	4.3064	2.9327	5.6476	7.3455	-0.3067	-0.1431	0.1776	-0.3619	-0.093	0.4074	-0.3437	-0.3632	0.405	0.1769	0.0467	-0.0223	0.3084	0.0097	0.3355	-12.7998	38.396	-47.3736
8	4.6528	4.22	-3.4561	7.3825	-6.346	8.9582	0.3476	0.1137	0.4759	-0.0289	-0.1056	0.3892	-0.6522	-0.3987	-0.3277	0.4329	0.1589	0.0245	0.3252	-0.0043	0.267	20.1474	16.7463	-17.7449
9	1.6812	0.3066	0.5003	2.2171	0.1449	3.1454	0.1048	-0.0932	0.269	0.0922	0.0981	-0.0564	-0.8038	0.0233	-0.1759	0.4908	0.0652	0.0029	0.2516	-0.0282	0.2117	29.0449	14.1304	-11.6593
10	1.1029	-1.5493	0.5047	2.0882	0.0867	1.9576	0.008	0.0437	0.2046	0.4943	0.13	-0.1152	-1.1014	-0.5545	-0.0998	0.469	0.0956	-0.0269	0.264	-0.0308	0.1954	26.4127	10.6768	-15.1037
11	-0.0019	0.223	-0.305	2.7042	-5.0027	9.124	-0.2172	-0.1806	-0.1203	0.3418	0.1914	0.1482	-0.2949	-0.3513	-0.0687	0.3857	0.1093	0.0163	0.2582	0.0341	0.2796	25.5315	20.5693	-34.1101
12	2.1256	-0.3449	0.4294	7.011	2.9477	3.3975	0.097	0.3803	-0.1972	-0.2132	0.1525	-0.6165	0.1627	0.4402	-0.1146	0.1794	-0.0028	0.0495	0.332	-0.0493	0.2825	34.0846	0.018	-55.3059
13	0.7625	1.4713	1.5209	6.5224	4.8873	4.3151	-0.1778	-0.1631	0.099	-0.2772	0.1628	0.08	-0.1943	-0.2999	0.0397	0.1694	-0.0502	-0.0086	0.2607	0.0227	0.271	24.9943	10.125	-48.81
14	0.2839	0.4573	0.3789	1.8704	1.6605	1.3402	-0.0148	0.4557	0.1659	-0.0187	0.2821	0.2934	-0.0863	0.4895	-0.1234	0.1721	-0.051	-0.0352	0.3628	0.028	0.252	19.9506	3.6779	-52.9602
15	1.0462	0.5692	0.7692	4.4581	2.4159	3.6332	-0.1879	0.1556	0.0478	-0.327	0.2006	0.0558	-0.2297	0.1307	-0.0325	0.1289	-0.0386	-0.0191	0.2945	0.0235	0.2349	26.7573	8.4873	-53.0501
16	2.3128	0.5149	0.99	1.6272	0.3264	5.0189	-0.0162	-0.105	-0.1653	-0.0819	0.0652	-0.022	0.347	0.0232	-0.0726	0.2425	0.0468	-0.0027	0.1842	0.0181	0.2144	33.0781	-7.6593	-13.1239
17	1.4702	-0.0428	-0.1816	0.8195	0.8345	4.4462	-0.0541	0.0607	-0.134	0.1309	-0.0219	-0.0714	0.0655	-0.1114	0.067	0.1625	0.0635	0.0064	0.1369	-0.004	0.1984	34.5779	-3.1248	-34.5386
18	0.8478	1.0629	-1.0684	4.4283	-1.4511	2.2863	-0.0103	-0.0228	0.0234	-0.0128	-0.06	-0.2283	0.1178	0.1869	0.0923	0.1159	-0.0028	-0.025	0.2383	-0.0256	0.1998	39.138	0.7932	-43.1406
19	4.4703	-3.8047	0.4564	8.0713	0.1596	4.4881	-0.0738	-0.1233	0.1081	-0.3134	-0.1452	-0.3709	0.2164	0.6475	0.1856	0.2923	0.0053	0.0471	0.3565	0.1174	0.3763	8.2418	35.3384	-30.4944
20	4.3105	-3.5756	-0.5008	7.967	-0.4235	5.1044	0.5285	0.2083	-0.5424	-0.7134	-0.6146	0.6377	-0.1162	-0.7438	0.1288	0.4513	0.072	-0.0965	0.3377	-0.1009	0.3431	24.3783	3.9683	-28.1827

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 150 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 151 through 213 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 17 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 130 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 131 through 194 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 195 through 220 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 25 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 26 through 75 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 76 through 101 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 102 through 113 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 114 through 128 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 129 through 150 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 151 through 163 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 164 through 213 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 105 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 106 through 140 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 141 through 220 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 12 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 1 through 12 )

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