PDB-5iv2: Cetuximab Fab in complex with Arg9Cir meditope variant

ID or keywords:

Entry

Database: PDB / ID: 5iv2

Title

Cetuximab Fab in complex with Arg9Cir meditope variant

Components

Cetuximab Fab, heavy chain
Cetuximab Fab, light chain
Meditope variant

Keywords

IMMUNE SYSTEM

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: 2.481 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	Mar 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	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 1.2	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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5iv2.cif.gz	361 KB	Display	PDBx/mmCIF format
PDB format	pdb5iv2.ent.gz	293.9 KB	Display	PDB format
PDBx/mmJSON format	5iv2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5iv2_validation.pdf.gz	460.9 KB	Display	wwPDB validaton report
Full document	5iv2_full_validation.pdf.gz	464.9 KB	Display
Data in XML	5iv2_validation.xml.gz	38.3 KB	Display
Data in CIF	5iv2_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/5iv2 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/5iv2	HTTPS FTP

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Related structure data

Related structure data	5etuC 5eukC 5f88C 5ff6C 5i2iC 5iopC 5ir1C 5itfC 5ivzC 5t1kC 5t1lC 5t1mC 5th2C 4gw1S 5esq 5hpm 5hyq 5icx 5icy 5icz 5id0 5id1 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5icz-1 6azl-2 6azk-1 5tjd-d 5t1m-2 5f88-1 5itf-2 4gw1-2 5euk-1 3vfg-d 6y1n-d 4kk5-3 1bbj-1 6z3k-9 5id0-2 1ejo-d 5t1l-2 5hyq-1 5etu-2 5t1m-1 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: Meditope variant

F: Meditope variant

hetero molecules

97.3 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 variant

hetero molecules

defined by author
48.7 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 variant

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.140, 83.190, 212.460
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 variant Mass: 1380.551 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.: 5 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.93 Å³/Da / Density % sol: 57.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.4 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 7, 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: 2.48→33.156 Å / Num. obs: 40884 / % possible obs: 99.3 % / Redundancy: 5.8 % / Net I/σ(I): 29.2
Reflection shell	Resolution: 2.48→2.55 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 8.3 / % possible all: 93.2

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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: 2.481→33.156 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.39

	R_factor	Num. reflection	% reflection
R_free	0.2105	2045	5 %
R_work	0.1647	-	-
obs	0.167	40876	99.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å

Refinement step

Cycle: LAST / Resolution: 2.481→33.156 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6714	0	25	617	7356

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6963
X-RAY DIFFRACTION	f_angle_d	0.644	9502
X-RAY DIFFRACTION	f_dihedral_angle_d	11.063	4152
X-RAY DIFFRACTION	f_chiral_restr	0.045	1067
X-RAY DIFFRACTION	f_plane_restr	0.004	1218

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 (%)
2.4813-2.539	0.2972	124	0.2051	2347	X-RAY DIFFRACTION	92
2.539-2.6024	0.2414	135	0.1922	2559	X-RAY DIFFRACTION	100
2.6024-2.6728	0.2717	136	0.1851	2588	X-RAY DIFFRACTION	100
2.6728-2.7514	0.2092	133	0.1869	2537	X-RAY DIFFRACTION	100
2.7514-2.8401	0.2534	136	0.1823	2580	X-RAY DIFFRACTION	100
2.8401-2.9416	0.2771	135	0.1833	2561	X-RAY DIFFRACTION	100
2.9416-3.0593	0.2103	136	0.1773	2587	X-RAY DIFFRACTION	100
3.0593-3.1984	0.2327	137	0.1768	2593	X-RAY DIFFRACTION	100
3.1984-3.3669	0.1899	135	0.1717	2570	X-RAY DIFFRACTION	100
3.3669-3.5776	0.1814	137	0.1502	2601	X-RAY DIFFRACTION	100
3.5776-3.8535	0.1929	136	0.1483	2595	X-RAY DIFFRACTION	100
3.8535-4.2405	0.2184	138	0.1385	2622	X-RAY DIFFRACTION	100
4.2405-4.8525	0.1652	138	0.1204	2626	X-RAY DIFFRACTION	100
4.8525-6.1074	0.1602	141	0.1547	2670	X-RAY DIFFRACTION	100
6.1074-33.1585	0.2325	148	0.1997	2795	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	1.3591	0.1511	0.7523	1.8738	-0.3519	2.0052	0.0195	-0.0265	0.1383	-0.0012	0.0619	0.0341	-0.2664	0.0424	-0.0908	0.1731	0.0121	0.0347	0.1261	-0.032	0.1033	25.1495	-26.8303	-15.9334
2	0.1009	0.2436	-0.4174	0.9548	-1.7514	3.2254	-0.0212	-0.0059	0.0266	0.2226	0.1843	0.0891	-0.1977	0.0377	-0.0555	0.2327	0.0184	0.0302	0.0811	0.0148	0.1482	24.7009	-18.3299	-35.3859
3	1.4728	-0.1219	0.3971	3.2775	1.4272	3.1761	0.0226	0.0764	-0.1609	0.0734	0.0102	0.0453	0.365	-0.0173	-0.0157	0.0843	-0.0128	0.0125	0.1098	0.0069	0.139	28.4466	-30.9171	-53.7767
4	2.9681	0.6785	1.5043	0.8981	1.8948	3.9708	-0.0642	0.0641	0.3174	-0.007	-0.1443	0.1604	-0.12	-0.2352	0.152	0.1008	-0.0451	-0.0262	0.2105	-0.0109	0.216	19.7633	-33.7303	-55.7426
5	1.7765	-0.6971	0.594	2.5106	0.5523	1.5706	0.1675	0.2227	-0.0587	-0.3014	-0.1762	0.122	0.1035	-0.0149	0.0195	0.1019	0.0109	0.0166	0.1646	-0.0156	0.1424	26.6059	-28.527	-55.1082
6	3.2805	0.7855	1.996	2.3662	1.148	5.6335	0.0008	-0.0565	-0.074	0.0095	-0.0316	-0.2426	0.292	0.2727	0.0083	0.1258	0.0601	0.0067	0.1745	0.0179	0.1427	38.3466	-48.291	-20.5009
7	1.5868	0.1225	0.3315	1.5291	0.1605	3.5956	0.0259	-0.1178	-0.1525	0.0365	0.0441	0.0552	0.3703	-0.0596	-0.0586	0.1473	-0.0193	0.0022	0.089	0.002	0.1182	31.313	-47.0253	-16.2494
8	1.9648	1.2948	-0.3263	3.1368	-0.2678	1.9061	-0.0336	-0.1662	0.0649	-0.052	-0.0747	0.043	0.0917	-0.0656	0.1052	0.0621	0.0138	0.0034	0.1067	-0.0296	0.1498	36.0177	-37.1824	-45.9067
9	3.2862	1.8209	-1.1459	6.4571	-3.2359	3.4479	-0.0443	-0.2083	-0.2188	-0.1508	-0.1762	-0.4224	0.1335	0.2999	0.2348	0.0638	0.0502	0.0176	0.1577	0.0113	0.1736	44.9816	-38.702	-47.5488
10	3.0526	2.7299	2.2296	2.9485	2.5979	4.8118	0.2408	-0.0137	-0.2422	-0.0325	-0.0945	-0.3534	0.2206	0.0786	-0.1544	0.1682	0.0856	0.0307	0.1997	0.0052	0.1715	12.0336	-16.9757	-17.5108
11	1.1934	-0.1368	-1.3627	2.2923	0.0888	2.7619	-0.015	0.0223	-0.1029	0.0504	0.1504	0.1188	0.1047	-0.3177	-0.1259	0.1225	0.0197	0.0035	0.1148	0.0293	0.138	2.059	-13.5478	-11.7746
12	1.4777	-0.3362	0.3783	1.1106	0.5806	2.5118	-0.0419	-0.0331	-0.1784	-0.0356	0.1093	-0.0168	0.0509	-0.0422	-0.1042	0.1931	0.0242	0.0003	0.1382	0.0148	0.0832	5.921	-12.4685	-14.6333
13	0.1229	0.5513	1.0869	2.5762	5.0153	9.8008	-0.1286	-0.0626	0.1121	0.1983	0.0168	-0.0715	0.2953	0.0912	0.1634	0.2357	0.0168	-0.001	0.1187	-0.0095	0.1739	6.4266	-20.764	-34.2349
14	2.6813	0.2232	-0.9464	2.1173	0.5388	3.2761	0.2047	0.4418	0.302	-0.2518	-0.122	0.1112	-0.3832	-0.3269	-0.0459	0.1015	-0.0071	-0.0084	0.2044	0.0145	0.1401	-2.3942	0.2791	-55.408
15	0.1566	0.6575	-0.5226	2.7646	-2.2037	1.7647	-0.0476	-0.0318	-0.0866	-0.0112	-0.0035	-0.1846	0.0002	0.0855	0.0707	0.0774	-0.0247	0.004	0.1285	-0.0018	0.2209	7.0629	-10.2415	-48.8778
16	1.6726	0.5488	-0.6363	1.0633	-1.4842	2.075	-0.0361	0.2184	-0.1835	-0.0625	0.1482	-0.1004	0.158	-0.267	-0.1781	0.0714	0.0012	0.0128	0.1958	-0.0527	0.1904	12.0865	-3.7406	-53.0243
17	1.2535	0.6531	-0.5379	2.4176	-0.9124	2.2426	-0.1518	0.1671	-0.0519	-0.2564	0.1219	-0.0477	0.1653	-0.0677	0.0299	0.0917	-0.0009	0.0275	0.1651	-0.015	0.1157	5.2229	-8.7628	-53.0789
18	1.5556	0.173	-0.4234	1.9465	0.0573	3.4019	-0.0109	-0.0404	0.1696	0.0278	0.0895	0.0069	-0.3686	-0.1492	-0.068	0.1546	0.04	0.0028	0.1216	-0.0061	0.1191	-1.2098	7.0378	-13.8715
19	1.7861	-0.3527	-0.3872	1.7748	-1.8009	2.143	-0.1628	0.0374	-0.1049	-0.45	0.0682	-0.2609	-0.4571	-0.0061	0.0524	0.0803	-0.0068	0.0334	0.1007	0.0208	0.0964	-2.8861	5.861	-45.5357
20	1.3232	0.6693	0.7233	2.9187	0.2198	1.2993	0.0189	0.0061	-0.0416	-0.0537	-0.0429	0.1516	-0.0841	-0.1568	-0.0069	0.0714	0.001	0.0127	0.1534	0.0159	0.1194	-7.214	-0.9308	-43.2991
21	1.4335	-1.4461	-2.1758	2.3496	1.2622	4.2925	-0.1148	0.1408	-0.4642	-0.854	-0.0076	0.084	-0.241	-0.2059	0.0257	0.1664	0.0197	-0.0045	0.202	-0.0316	0.2311	23.9264	-35.617	-30.9086
22	0.9426	-1.5851	-0.1532	2.6856	0.5473	4.7525	0.1014	0.0307	0.1815	-0.4953	-0.1153	0.0539	0.0105	0.2567	0.0625	0.1889	0.0545	0.0555	0.2079	0.0301	0.1984	7.6299	-3.9539	-28.309

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:101)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 102:113)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 114:150)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 151:163)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 164:213)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 1:33)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 34:117)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 118:194)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 195:220)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 1:25)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 26:69)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 70:101)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 102:113)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 114:128)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 129:150)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 151:163)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 164:213)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 1:117)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 118:140)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 141:220)
21	X-RAY DIFFRACTION	21	chain 'E'
22	X-RAY DIFFRACTION	22	chain 'F'

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