PDB-5u3d: STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT

ID or keywords:

Entry

Database: PDB / ID: 5u3d

Title

STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT

Components

(MEMAB TRASTUZUMAB FAB ...) x 2
Immunoglobulin G binding protein A
Protein L

Keywords

IMMUNE SYSTEM

Function / homology

Function and homology information

IgG binding /

immunoglobulin binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Finegoldia magna (bacteria)

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Bzymek, K.P. / Avery, K.N. / Zer, C. / Williams, J.C.

Citation

Journal: To Be Published
Title: Meditope Enabled Trastuzumab I83E Variant
Authors: Bzymek, K.P. / Avery, K.N. / Zer, C. / Williams, J.C.

History

Deposition	Dec 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_assembly_prop / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name ..._entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2	Apr 18, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3	Oct 4, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u3d.cif.gz	249.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5u3d.ent.gz	198.9 KB	Display	PDB format
PDBx/mmJSON format	5u3d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/5u3d ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u3d	HTTPS FTP

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Related structure data

Related structure data	4ioiS 5u5f 5u5m 5u6a S: Starting model for refinement
Similar structure data	1ejv-d 6z5f-2 4g9i-1 5epv-d 4yqx-d 5zoi-d 6u44-1 4410 6tkz-2 2p1n-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E

B: MEMAB TRASTUZUMAB FAB HEAVY CHAIN

E: Protein L

C: Immunoglobulin G binding protein A

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	52.850, 104.650, 116.880
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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Protein , 1 types, 1 molecules E

#3: Protein	Protein L / Mass: 6994.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918

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Antibody , 3 types, 3 molecules ABC

#1: Antibody	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E Mass: 23518.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	MEMAB TRASTUZUMAB FAB HEAVY CHAIN Mass: 23774.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody	Immunoglobulin G binding protein A Mass: 6037.530 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UW42, UniProt: P02976*PLUS

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Non-polymers , 2 types, 804 molecules

#5: Chemical	ChemComp-MRY / MESO-ERYTHRITOL / Erythritol Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 803 / 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: 2.69 Å³/Da / Density % sol: 54.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 7.2

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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: Sep 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.77→33.43 Å / Num. obs: 63311 / % possible obs: 99.3 % / Redundancy: 4.5 % / R_merge(I) obs: 0.075 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.77→1.82 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.76 / Mean I/σ(I) obs: 1.88 / Num. unique all: 4259 / % possible all: 91.1

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	dev_1839	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IOI

4ioi

Resolution: 1.77→33.43 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.61

	R_factor	Num. reflection	% reflection
R_free	0.185	3166	5 %
R_work	0.157	-	-
obs	0.158	63311	99.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.77→33.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4212	0	8	803	5023

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4470
X-RAY DIFFRACTION	f_angle_d	1.048	6107
X-RAY DIFFRACTION	f_dihedral_angle_d	12.869	1624
X-RAY DIFFRACTION	f_chiral_restr	0.046	678
X-RAY DIFFRACTION	f_plane_restr	0.005	806

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 (%)
1.7721-1.7985	0.2971	116	0.281	2209	X-RAY DIFFRACTION	85
1.7985-1.8266	0.3029	137	0.2442	2594	X-RAY DIFFRACTION	99
1.8266-1.8566	0.2368	137	0.216	2606	X-RAY DIFFRACTION	100
1.8566-1.8886	0.2255	138	0.191	2613	X-RAY DIFFRACTION	100
1.8886-1.9229	0.2529	134	0.1873	2554	X-RAY DIFFRACTION	100
1.9229-1.9599	0.2305	138	0.1719	2625	X-RAY DIFFRACTION	100
1.9599-1.9999	0.1703	136	0.1678	2577	X-RAY DIFFRACTION	100
1.9999-2.0434	0.2273	138	0.1626	2625	X-RAY DIFFRACTION	100
2.0434-2.0909	0.2212	137	0.1668	2601	X-RAY DIFFRACTION	100
2.0909-2.1432	0.1931	137	0.1562	2600	X-RAY DIFFRACTION	100
2.1432-2.2011	0.1818	138	0.1518	2621	X-RAY DIFFRACTION	100
2.2011-2.2659	0.2063	136	0.1543	2583	X-RAY DIFFRACTION	100
2.2659-2.339	0.2028	138	0.1519	2633	X-RAY DIFFRACTION	100
2.339-2.4226	0.1648	138	0.1516	2627	X-RAY DIFFRACTION	100
2.4226-2.5196	0.1729	139	0.1589	2631	X-RAY DIFFRACTION	100
2.5196-2.6342	0.1943	138	0.1554	2620	X-RAY DIFFRACTION	100
2.6342-2.773	0.2207	138	0.1568	2636	X-RAY DIFFRACTION	100
2.773-2.9466	0.1876	139	0.1544	2642	X-RAY DIFFRACTION	100
2.9466-3.174	0.1795	140	0.1584	2655	X-RAY DIFFRACTION	100
3.174-3.4931	0.1514	140	0.1457	2660	X-RAY DIFFRACTION	100
3.4931-3.9978	0.1388	141	0.1353	2676	X-RAY DIFFRACTION	100
3.9978-5.0341	0.1458	143	0.1219	2715	X-RAY DIFFRACTION	100
5.0341-33.4323	0.1857	150	0.1662	2842	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	0.6966	-0.0685	-0.2827	1.3466	0.7569	1.579	0.0076	0.0281	0.0503	-0.0165	0.022	-0.0356	-0.1085	-0.0593	-0.0262	0.0866	0.006	-0.0074	0.106	0.0123	0.0997	-12.8837	29.4554	9.6319
2	0.6862	1.0307	1.4514	1.6968	2.2938	3.122	0.0121	-0.0344	-0.0373	-0.1086	-0.0166	-0.0344	-0.333	-0.0482	0.0444	0.1415	0.0129	-0.0102	0.1282	0.0096	0.1377	-6.5756	37.4126	26.8364
3	2.7087	-1.9623	1.1795	3.9285	-0.8521	1.6609	0.0532	0.0519	-0.0875	0.1742	0.0702	-0.1352	0.1609	0.1865	-0.1146	0.1647	0.0239	-0.0333	0.1611	-0.0442	0.1251	4.704	25.8943	42.5284
4	2.5015	-1.2701	1.5868	2.1459	-0.7705	2.9247	0.1376	-0.077	-0.0281	-0.0407	0.0204	-0.1229	0.0437	0.2132	-0.1366	0.1185	-0.0068	0.021	0.1299	-0.0339	0.0904	2.2822	28.9498	35.0962
5	3.3855	-1.6969	2.2007	2.2395	-2.0105	3.0853	0.0665	0.0241	-0.1594	0.2111	0.0514	-0.328	0.2384	0.4001	-0.0331	0.2593	0.1046	-0.0974	0.2458	-0.0696	0.2335	13.0519	19.725	45.2049
6	2.988	-2.4437	2.2027	4.4585	-2.3858	3.5919	-0.0979	-0.1738	0.1144	0.3883	0.1805	-0.4339	0.0212	0.1275	-0.0385	0.1843	0.02	-0.0495	0.159	-0.0392	0.1534	8.3195	32.4626	47.5099
7	0.663	0.376	0.801	1.2586	-0.3148	2.5089	-0.3027	-0.4171	-0.0718	0.2815	0.2907	0.0641	0.0369	-0.0692	0.0398	0.1385	0.0111	-0.0032	0.0906	0.0107	0.1137	-7.4885	4.2633	18.2618
8	4.0039	-2.9912	0.2296	2.9177	-1.138	1.8818	-0.0627	-0.012	-0.2977	0.049	0.1397	0.2111	0.1044	-0.1772	-0.0981	0.1221	-0.0229	-0.0055	0.115	0.0053	0.1966	-18.2343	3.8228	11.3476
9	1.9653	-0.2147	0.2172	2.8207	0.4052	2.9741	-0.0586	0.0424	0.1246	0.017	0.0991	-0.1442	-0.0861	0.0667	-0.0441	0.0719	0.0215	-0.0175	0.0891	0.0221	0.1151	-8.081	12.6174	8.9051
10	5.4816	0.0037	2.3426	2.1683	0.4602	3.0671	0.175	0.2826	-0.12	-0.2519	-0.1257	-0.1155	0.0612	0.2461	-0.0042	0.1604	0.0332	0.0178	0.1027	0.0123	0.0827	-7.3419	5.4978	0.679
11	1.6928	-1.4612	0.8342	2.0613	0.4148	2.696	-0.0496	0.2362	0.0092	0.0248	0.1464	0.0068	0.1007	0.0972	-0.1061	0.0995	0.0195	0.0038	0.0658	0.0077	0.1138	-6.9656	1.9546	10.435
12	4.5445	-0.7554	0.5778	2.4033	-0.5667	2.4263	-0.0105	0.1016	-0.0063	0.0682	0.0872	0.2616	-0.0762	-0.2461	-0.0917	0.0898	0.0056	0.0105	0.1136	-0.005	0.141	-16.8282	14.3734	10.8007
13	0.065	0.1177	0.0868	0.4785	0.7388	1.3359	0.0471	-0.0436	0.001	0.3489	0.1182	-0.1052	0.3801	0.2228	-0.1499	0.2361	0.0492	-0.0397	0.171	-0.0329	0.1534	0.7323	14.1252	37.8999
14	1.2225	-1.3187	-0.6474	2.269	1.5281	2.5108	0.0524	0.048	-0.133	0.2198	-0.0648	0.1527	0.366	-0.076	0.0336	0.1996	-0.0074	-0.0012	0.1331	-0.0255	0.1407	-5.2665	16.5371	39.5249
15	2.9376	-0.5048	-0.4821	1.8191	0.5959	0.775	-0.0186	-0.2846	-0.3338	0.9412	-0.0301	0.3202	0.7236	0.189	0.1556	0.5104	0.0202	0.048	0.1674	0.0127	0.2445	-5.7621	10.2664	46.8803
16	2.7846	-4.5681	-0.6175	8.4834	0.3992	4.7031	0.0983	-0.1098	-0.1787	0.1923	-0.0069	-0.2062	-0.1526	0.2831	-0.0933	0.1717	-0.0534	-0.0091	0.1238	-0.0025	0.2838	-0.4298	43.2755	15.1101
17	6.16	-1.8848	-2.4254	3.583	0.4543	2.7214	0.1271	0.2907	0.1676	-0.1147	-0.1073	-0.1232	-0.091	0.0698	-0.0575	0.1087	-0.0302	-0.0071	0.1024	0.0096	0.1452	-1.5857	41.422	8.3317
18	6.7036	-2.3217	-0.525	4.6448	0.4816	4.5091	0.1536	0.0083	0.6092	0.2509	0.0779	-0.1993	-0.5456	0.4455	-0.1578	0.2967	-0.0561	0.036	0.1898	0.0425	0.2623	0.509	50.1301	11.0492
19	6.3374	0.1773	-3.848	4.5582	0.1166	5.9579	0.2248	0.8149	0.1598	-0.5141	-0.1695	-0.776	-0.2615	0.7244	-0.014	0.2635	0.0169	0.0099	0.3667	0.0261	0.2688	-24.5024	13.635	56.8634
20	3.4529	-2.8532	-0.8546	2.6256	0.8399	1.4887	0.12	0.1173	0.1809	-0.1605	-0.0859	-0.0723	-0.0804	0.0434	-0.0226	0.1408	0.003	0.001	0.1025	0.0193	0.1325	-27.7512	8.4216	66.2335
21	2.7814	-1.4691	-3.977	3.5535	1.4312	5.8735	0.1527	0.1971	-0.2841	-0.5389	-0.235	0.4909	0.1009	-0.1209	0.0539	0.2312	0.0363	-0.0674	0.1773	-0.007	0.1442	-31.9048	3.373	60.2503

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 101 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 102 THROUGH 113 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 114 THROUGH 150 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 151 THROUGH 174 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 175 THROUGH 188 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 189 THROUGH 214 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 1 THROUGH 17 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 18 THROUGH 32 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 33 THROUGH 52 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 53 THROUGH 67 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 68 THROUGH 91 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 92 THROUGH 113 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 114 THROUGH 141 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 142 THROUGH 210 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 211 THROUGH 221 )
16	X-RAY DIFFRACTION	16	CHAIN 'E' AND (RESID 19 THROUGH 33 )
17	X-RAY DIFFRACTION	17	CHAIN 'E' AND (RESID 34 THROUGH 61 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 62 THROUGH 81 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 1 THROUGH 16 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 17 THROUGH 35 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 36 THROUGH 54 )

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Yorodumi