PDB-4gw5: cQYN meditope - Cetuximab Fab

ID or keywords:

Entry

Database: PDB / ID: 4gw5

Title

cQYN meditope - Cetuximab Fab

Components

Fab Heavy Chain
Fab Light Chain
cQYN meditope

Keywords

IMMUNE SYSTEM / IgG / EGFR

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Donaldson, J.M. / Zer, C. / Avery, K.N. / Bzymek, K.P. / Horne, D.A. / Williams, J.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies.
Authors: Donaldson, J.M. / Zer, C. / Avery, K.N. / Bzymek, K.P. / Horne, D.A. / Williams, J.C.

History

Deposition	Aug 31, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2013	Group: Database references
Revision 1.2	Nov 6, 2013	Group: Database references
Revision 1.3	Apr 9, 2014	Group: Source and taxonomy
Revision 1.4	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.5	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gw5.cif.gz	357.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4gw5.ent.gz	292.4 KB	Display	PDB format
PDBx/mmJSON format	4gw5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gw5_validation.pdf.gz	464.5 KB	Display	wwPDB validaton report
Full document	4gw5_full_validation.pdf.gz	468.1 KB	Display
Data in XML	4gw5_validation.xml.gz	38 KB	Display
Data in CIF	4gw5_validation.cif.gz	55.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/4gw5 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/4gw5	HTTPS FTP

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Related structure data

Related structure data	4gw1C 4hjgC 4hkzC 4ioiC 1yy9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3utz-2 5t1l-1 4r7n-4 5hpm-2 4kk5-3 5ivz-1 4gw1-2 5t1m-2 5t1m-1 4r4b-4 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Fab Light Chain

B: Fab Heavy Chain

C: Fab Light Chain

D: Fab Heavy Chain

E: cQYN meditope

F: cQYN meditope

hetero molecules

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

1

A: Fab Light Chain

B: Fab Heavy Chain

E: cQYN meditope

hetero molecules

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

2

C: Fab Light Chain

D: Fab Heavy Chain

F: cQYN meditope

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.160, 82.520, 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	Fab Light Chain Mass: 23448.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus,Homo sapiens
#2: Antibody	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
#3: Protein/peptide	cQYN meditope Mass: 1387.629 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H₂O

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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: 57.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 A were grown in 100 mM sodium phosphate/citrate, 2.5 M ...Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 A were grown in 100 mM sodium phosphate/citrate, 2.5 M sodium/potassium phosphate, 1.6 % w/v meso-erythritol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal

Density Matthews: 2.89 Å³/Da / Density % sol: 57.4 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 A were grown in 100 mM sodium phosphate/citrate, 2.5 M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2→29.61 Å / Num. all: 77043 / Num. obs: 76935 / % possible obs: 99.9 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Net I/σ(I): 19.57

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Processing

Software

Name	Version	Classification
Blu-Ice	Ice	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1yy9

1yy9

Resolution: 2.2→29.607 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 21.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2216	2000	3.45 %	random
R_work	0.1738	-	-	-
obs	0.1754	58047	99.97 %	-
all	-	58059	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.335 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1152 Å²	0 Å²	-0 Å²
2-	-	6.3242 Å²	-0 Å²
3-	-	-	-6.4394 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.607 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6715	0	15	618	7348

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6892
X-RAY DIFFRACTION	f_angle_d	1.102	9368
X-RAY DIFFRACTION	f_dihedral_angle_d	12.334	2443
X-RAY DIFFRACTION	f_chiral_restr	0.075	1058
X-RAY DIFFRACTION	f_plane_restr	0.004	1196

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 (%)
2.2-2.255	0.2511	140	0.1877	3946	X-RAY DIFFRACTION	100
2.255-2.316	0.2702	141	0.1908	3951	X-RAY DIFFRACTION	100
2.316-2.3841	0.2664	142	0.1966	3974	X-RAY DIFFRACTION	100
2.3841-2.461	0.2898	141	0.1949	3946	X-RAY DIFFRACTION	100
2.461-2.5489	0.2706	141	0.1911	3949	X-RAY DIFFRACTION	100
2.5489-2.6509	0.2377	142	0.1883	3948	X-RAY DIFFRACTION	100
2.6509-2.7715	0.2457	140	0.1849	3967	X-RAY DIFFRACTION	100
2.7715-2.9175	0.2443	143	0.1878	4000	X-RAY DIFFRACTION	100
2.9175-3.1001	0.2212	142	0.1819	3963	X-RAY DIFFRACTION	100
3.1001-3.3391	0.2324	143	0.1754	3994	X-RAY DIFFRACTION	100
3.3391-3.6746	0.1992	143	0.1696	4020	X-RAY DIFFRACTION	100
3.6746-4.205	0.1792	144	0.1502	4041	X-RAY DIFFRACTION	100
4.205-5.2929	0.1708	145	0.1334	4091	X-RAY DIFFRACTION	100
5.2929-29.6094	0.2465	153	0.2018	4257	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	2.3258	-1.5408	-0.6994	3.1315	2.5364	4.2732	0.2737	0.0272	0.1757	-0.2888	0.1303	-0.3815	-0.807	0.3301	-0.3445	0.4566	-0.0992	0.1164	0.303	-0.0089	0.2709	12.7446	17.6923	19.1156
2	0.954	-0.011	0.8996	2.5327	0.8995	2.332	0.0953	0.0633	0.1442	-0.2074	0.0797	-0.1554	-0.5995	-0.0277	-0.1684	0.3345	0.0019	0.071	0.2037	0.045	0.1801	4.8746	13.8542	14.3307
3	0.1424	-0.5198	-0.8448	3.4168	5.1433	7.7421	0.0492	0.0162	-0.0468	-0.5297	0.1527	-0.2061	-0.5345	0.0081	-0.2907	0.3055	-0.0294	0.0542	0.1565	0.0239	0.2012	7.2556	22.9372	34.9557
4	1.0402	-0.774	1.2564	2.9325	-0.968	3.1397	0.0753	-0.0759	0.0626	0.0244	-0.0582	-0.0514	0.1232	0.0292	-0.0002	0.113	0.0066	0.028	0.1967	0.0222	0.2285	5.6876	9.7349	53.8288
5	2.078	0.4595	0.7079	3.4646	-1.3314	2.9986	0.0997	-0.2866	0.0035	0.1614	-0.1114	-0.1394	0.0353	-0.1111	0.022	0.0688	0.0058	0.0157	0.2197	0.0022	0.1797	5.4091	13.0031	54.2553
6	3.1477	-1.2915	1.7887	2.7401	-1.2309	6.0578	-0.0261	-0.077	-0.1596	-0.063	0.2031	0.1078	0.4306	-0.406	-0.1379	0.1995	-0.0489	-0.0012	0.2699	-0.0033	0.2017	-6.48	-6.608	19.8701
7	0.5747	0.2098	-1.5723	5.2921	1.7131	5.5018	-0.0006	-0.0995	0.0555	0.2191	0.1854	-0.2105	0.165	0.4829	-0.2161	0.2645	0.0108	-0.0148	0.2246	0.0222	0.2031	4.8137	-2.5905	17.4317
8	1.3482	-0.0978	0.2055	1.5118	-0.0551	3.2678	0.016	0.0835	-0.1138	0.0598	0.0926	-0.0255	0.1946	-0.0027	-0.1083	0.2373	0.019	0.0058	0.201	0.0081	0.2014	-0.4083	-6.258	15.5206
9	2.7852	-0.4646	-0.4295	0.3546	0.0176	3.414	0.0303	-0.1268	0.4172	0.334	-0.1442	-0.0834	0.5042	-0.0368	-0.0293	0.0638	-0.0007	0.0265	0.1543	0.118	0.203	-3.4157	0.1153	48.7009
10	0.805	-0.8763	0.0202	1.8278	0.3772	1.2653	-0.0368	0.0704	0.0349	0.0396	-0.0588	-0.0553	0.0675	0.0588	0.0716	0.1328	0.0052	-0.0087	0.1946	0.0404	0.2472	-4.5031	5.7309	44.8152
11	2.7226	-0.288	0.3307	1.2534	-0.5037	1.1846	-0.0761	0.0048	-0.0861	0.2199	-0.102	0.1785	0.1048	-0.13	0.2472	0.1397	-0.0223	0.0056	0.226	-0.0037	0.2408	-12.6733	1.7943	46.7522
12	1.7478	0.6079	-0.0315	2.2884	0.0393	2.5576	0.0931	0.0197	-0.0879	0.0552	0.2585	0.2139	0.379	-0.4206	-0.3246	0.2646	-0.0572	-0.021	0.2577	0.0079	0.217	22.1649	26.661	14.5936
13	1.5568	0.3235	-0.8429	2.4087	-0.5939	2.791	-0.0449	0.132	-0.143	-0.2109	0.0853	-0.0879	0.5366	0.1025	-0.0895	0.3526	0.0063	-0.028	0.1872	-0.0359	0.1845	30.8446	25.4851	12.779
14	1.1133	0.0936	-0.2718	2.7948	-1.3953	3.7525	0.017	0.0637	-0.1949	-0.1579	0.2839	0.0974	0.3771	-0.286	-0.259	0.2886	-0.0702	-0.0115	0.2234	-0.0386	0.1862	26.5074	30.4313	15.1668
15	0.1604	-0.316	1.06	0.9128	-2.8521	8.9304	-0.1101	0.2062	0.0954	-0.2801	0.1379	0.0784	0.144	0.0203	-0.0884	0.3021	-0.055	-0.0044	0.2028	-0.0047	0.2428	25.689	20.598	34.0785
16	2.1238	-1.0969	-0.621	6.2454	1.1434	2.3308	-0.025	-0.4081	0.2638	0.0024	0.2115	-0.3902	-0.2505	0.3487	-0.1853	0.1532	-0.0355	0.0046	0.2957	-0.0317	0.1864	34.0978	41.026	55.4775
17	1.4071	-1.3987	-1.3471	4.5085	4.0305	3.5152	-0.1681	0.0666	-0.1079	0.0788	-0.0621	0.4424	0.1052	-0.2529	0.236	0.1563	0.006	-0.006	0.1851	0.0165	0.2321	25.0655	30.9129	48.8153
18	1.7578	-0.8563	-0.4286	1.9907	1.3293	1.418	-0.1383	-0.2868	-0.0521	-0.0057	0.2064	0.3511	0.1877	-0.0086	-0.0253	0.15	-0.0069	0.0218	0.2385	0.0164	0.2084	20.0277	37.3229	53.0077
19	1.4222	-0.5128	-0.5797	3.1237	2.697	4.0874	-0.1613	-0.2037	-0.1046	0.0624	-0.0075	0.2643	0.0346	0.192	0.1126	0.0757	0.0025	0.0226	0.1748	0.0243	0.164	27.0284	34.0696	50.7384
20	1.3533	-1.6072	-1.6598	3.8414	0.6366	2.984	-0.2766	-0.1841	-0.2169	1.0149	0.2503	-0.3478	0.745	0.146	-0.0681	0.2375	0.1181	0.0473	0.3107	0.094	0.1358	26.9547	27.4917	58.1958
21	0.994	-0.5439	-0.3102	1.2986	-0.1316	3.8579	-0.0262	0.0214	0.1185	0.0674	0.0753	0.0077	-0.4168	0.0401	-0.0558	0.2587	-0.042	0.0115	0.1737	-0.012	0.1826	33.1965	48.2278	14.1011
22	1.8728	0.4101	-0.2017	1.3745	1.7908	2.6033	-0.1907	-0.1063	-0.3235	0.4789	0.215	0.027	-0.624	-0.0119	-0.1222	-0.0101	0.0099	0.0299	0.0931	-0.0043	0.1473	35.0616	46.1119	45.9588
23	1.0297	-0.4341	0.841	2.965	-0.598	2.0774	-0.0052	-0.0199	-0.0259	0.0202	0.0182	-0.2084	-0.1268	0.1148	0.008	0.0947	-0.007	0.0381	0.1783	-0.0372	0.1931	39.2892	40.3254	43.45
24	4.6235	-3.9749	-1.8574	8.5157	-1.6045	2.7494	0.0223	0.6901	0.2325	0.0693	-0.0188	-0.5084	-0.973	1.0409	-0.0051	0.5011	-0.2002	-0.0639	0.6774	0.077	0.3344	8.6731	5.7965	30.9306
25	5.8347	-2.8272	2.9264	8.3317	2.0884	3.2279	-0.5865	0.2255	-0.2508	0.6513	0.3218	0.2171	-0.2757	-0.1425	0.2128	0.5974	-0.2133	0.0864	0.8302	-0.0691	0.458	23.8044	37.2656	28.9498

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:25)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 26:101)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 102:113)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 114:163)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 164:212)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 1:33)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 34:51)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 52:117)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 118:140)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 141:196)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 197:220)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 1:38)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 39:75)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 76:101)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 102:113)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 114:128)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 129:150)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 151:163)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 164:198)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 199:213)
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 1:117)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 118:140)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 141:220)
24	X-RAY DIFFRACTION	24	CHAIN E AND (RESSEQ 1:12)
25	X-RAY DIFFRACTION	25	CHAIN F AND (RESSEQ 1:12)

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