PDB-5u6a: CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO...

ID or keywords:

Entry

Database: PDB / ID: 5u6a

Title

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE

Components

Heavy Chain
Immunoglobulin G binding protein A
Light Chain
Protein L
meditope peptide

Keywords

IMMUNE SYSTEM / ANTIBODY / ANTIBODY-DRUG CONJUGATES

Function / homology

Function and homology information

cell envelope / IgG binding / immunoglobulin binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Finegoldia magna (bacteria)

Staphylococcus aureus (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.736 Å

Authors

Williams, J.C. / Bzymek, K.P. / Pucket, J. / Avery, K.A. / Ma, Y. / Xie, J. / Zer, C. / Horne, D.

Citation

Journal: To Be Published
Title: Crystal Structure Of I83E Meditope-Enabled Trastuzumab With Azido-PEG3-Meditope
Authors: Williams, J.C. / Bzymek, K.P. / Pucket, J. / Avery, K.A. / Ma, Y. / Xie, J. / Zer, C. / Horne, D.

History

Deposition	Dec 7, 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_entity_src_syn / pdbx_struct_assembly_prop / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen 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 / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
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
Revision 1.4	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u6a.cif.gz	266.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5u6a.ent.gz	212.6 KB	Display	PDB format
PDBx/mmJSON format	5u6a.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/u6/5u6a ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u6a	HTTPS FTP

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Related structure data

Related structure data	4ioiS 5u3d 5u5f 5u5m S: Starting model for refinement
Similar structure data	4ioi-d 6bae-d 5u5f-d 6b9y-d 5u5m-d 4hkz-d 4q47-1 6b9z-d 4hjg-d 6bah-d 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: Light Chain

B: Heavy Chain

E: Protein L

C: Immunoglobulin G binding protein A

D: meditope peptide

hetero molecules

62.2 kDa, 5 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)	53.250, 105.170, 117.070
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 , 3 types, 3 molecules ABC

#1: Antibody	Light Chain 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	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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Protein / Protein/peptide , 2 types, 2 molecules ED

#3: Protein	Protein L Mass: 6850.605 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
#5: Protein/peptide	meditope peptide Mass: 1851.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 858 molecules

#6: Chemical	ChemComp-MRY / MESO-ERYTHRITOL Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.65 Å³/Da / Density % sol: 53.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350 200 MM NACL, PH 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: Dec 12, 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: 1.736→31.526 Å / Num. obs: 65702 / % possible obs: 95.6 % / Redundancy: 2.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.062 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.736→1.78 Å / Redundancy: 2 % / R_merge(I) obs: 0.485 / Mean I/σ(I) obs: 2.24 / Num. unique all: 3974 / CC_1/2: 0.79 / % possible all: 76.5

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ioi

4ioi

Resolution: 1.736→31.526 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.47

	R_factor	Num. reflection	% reflection
R_free	0.1875	3285	5 %
R_work	0.1594	-	-
obs	0.1609	65699	95.63 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.736→31.526 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4354	0	8	857	5219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4744
X-RAY DIFFRACTION	f_angle_d	1.098	6489
X-RAY DIFFRACTION	f_dihedral_angle_d	11.893	2891
X-RAY DIFFRACTION	f_chiral_restr	0.053	713
X-RAY DIFFRACTION	f_plane_restr	0.005	859

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 (%)
1.7361-1.762	0.2686	105	0.2485	1988	X-RAY DIFFRACTION	71
1.762-1.7895	0.2606	135	0.2343	2566	X-RAY DIFFRACTION	93
1.7895-1.8188	0.2461	147	0.2183	2784	X-RAY DIFFRACTION	99
1.8188-1.8502	0.2551	147	0.2023	2790	X-RAY DIFFRACTION	100
1.8502-1.8838	0.2509	146	0.1913	2775	X-RAY DIFFRACTION	99
1.8838-1.9201	0.2185	147	0.1823	2806	X-RAY DIFFRACTION	99
1.9201-1.9593	0.2205	146	0.1784	2774	X-RAY DIFFRACTION	99
1.9593-2.0019	0.1893	147	0.1691	2778	X-RAY DIFFRACTION	99
2.0019-2.0484	0.1963	148	0.1718	2813	X-RAY DIFFRACTION	99
2.0484-2.0996	0.1973	145	0.1634	2768	X-RAY DIFFRACTION	99
2.0996-2.1564	0.1878	148	0.156	2799	X-RAY DIFFRACTION	99
2.1564-2.2198	0.1951	148	0.156	2821	X-RAY DIFFRACTION	99
2.2198-2.2915	0.1834	146	0.1551	2765	X-RAY DIFFRACTION	99
2.2915-2.3733	0.1845	146	0.1578	2780	X-RAY DIFFRACTION	99
2.3733-2.4683	0.1994	147	0.1597	2800	X-RAY DIFFRACTION	99
2.4683-2.5806	0.2362	146	0.1602	2773	X-RAY DIFFRACTION	98
2.5806-2.7166	0.1631	145	0.1581	2754	X-RAY DIFFRACTION	97
2.7166-2.8867	0.1998	144	0.1572	2726	X-RAY DIFFRACTION	96
2.8867-3.1094	0.2023	144	0.1587	2746	X-RAY DIFFRACTION	96
3.1094-3.422	0.182	142	0.1459	2698	X-RAY DIFFRACTION	94
3.422-3.9163	0.1524	141	0.1348	2669	X-RAY DIFFRACTION	92
3.9163-4.9311	0.1227	139	0.123	2652	X-RAY DIFFRACTION	90
4.9311-31.531	0.1773	136	0.1693	2589	X-RAY DIFFRACTION	85

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	0.6788	-0.0083	-0.9899	4.2188	-5.0364	7.4586	0.0549	0.0042	0.0022	0.041	0.1352	0.0527	-0.26	-0.1032	-0.2289	0.1353	0.0028	-0.0016	0.0955	-0.0257	0.1207	-19.3176	34.2462	-10.0221
2	1.8703	0.3309	0.1638	1.7526	-0.6949	0.9472	0.0198	-0.0714	0.0815	-0.013	0.0006	-0.1298	-0.0922	0.156	-0.0312	0.0471	-0.0104	-0.0034	0.099	-0.0068	0.1022	-10.2333	28.6833	-8.2397
3	0.2214	-0.2006	0.3607	0.4894	-0.6368	1.5646	0.0182	0.0208	-0.0033	-0.0341	0.057	0.0132	0.0355	-0.0166	-0.0418	0.0672	-0.0223	0.0023	0.0899	-0.0059	0.0854	-21.1355	26.6762	-25.749
4	4.7932	3.849	2.6188	3.9264	2.9332	2.9657	0.1105	-0.1759	0.1075	0.1408	-0.0688	0.1771	0.1781	-0.3094	-0.0346	0.1222	-0.0285	-0.0108	0.1217	0.0444	0.079	-31.5547	30.7912	-38.7358
5	3.4839	1.6753	1.557	3.1753	0.4276	3.169	0.2103	-0.1167	-0.1322	0.2094	0.0103	-0.1652	0.1096	-0.1692	-0.2095	0.0924	-0.0076	0.0305	0.0972	0.0214	0.064	-28.8086	29.3917	-35.2577
6	3.2493	2.3421	1.7071	3.7435	1.8455	3.0096	0.1955	-0.1416	-0.0764	-0.1751	0.0113	0.4593	0.3853	-0.627	0.0326	0.2087	-0.1342	-0.1128	0.2564	0.0804	0.195	-40.1585	20.1376	-45.0998
7	3.0948	3.3129	3.0516	5.8845	2.9609	4.1035	-0.0323	0.067	0.0114	-0.3215	0.2134	0.3194	0.1679	-0.1849	-0.0443	0.122	-0.0427	-0.0502	0.1294	0.0286	0.1258	-35.3104	32.7436	-47.6955
8	2.9161	0.4709	0.7585	1.6663	-0.0026	1.9443	-0.3373	0.3535	0.0512	-0.3493	0.313	-0.0766	0.0467	0.1372	0.024	0.109	-0.0046	0.0019	0.0878	-0.0177	0.0923	-19.1555	4.4342	-18.0373
9	3.0327	0.9283	0.7084	1.6051	0.4915	2.0652	0.0429	-0.2386	-0.2967	-0.0067	0.0074	-0.4082	0.1016	0.3233	-0.1396	0.065	0.0102	-0.0108	0.1559	0.0173	0.1947	-7.7226	3.9782	-11.1928
10	2.5706	-1.9804	2.313	3.3855	-2.3046	4.5292	0.0479	-0.1223	0.0025	0.2453	0.0281	0.1019	-0.1303	0.0021	-0.0842	0.0871	-0.045	-0.0167	0.0909	-0.0058	0.1109	-18.3423	12.2688	-7.668
11	7.4298	-0.6027	2.0929	1.1934	-0.0059	2.2913	0.221	-0.4943	0.1343	0.2295	-0.1766	-0.1214	0.0862	-0.1302	-0.0432	0.1649	-0.062	-0.0132	0.115	0.0094	0.0962	-18.4788	5.1114	-0.2734
12	2.2218	1.4637	1.0915	2.3299	-1.0502	2.8512	0.1395	-0.1961	-0.145	0.0253	0.0139	-0.0593	0.0985	-0.0723	-0.149	0.0917	-0.0225	-0.004	0.049	-0.0044	0.0782	-20.1779	2.0955	-10.2275
13	3.6593	0.8149	1.1732	2.7942	-0.0047	3.795	0.0604	-0.3092	0.2851	0.0868	-0.0707	-0.4763	-0.1663	0.4369	0.059	0.1004	-0.021	-0.0027	0.1537	-0.023	0.2052	-9.4287	14.8226	-9.6011
14	0.1858	-0.4524	-0.0601	1.1235	-0.3738	3.1857	-0.1376	0.0645	0.0703	-0.42	0.135	0.1324	0.1994	-0.2416	-0.0526	0.1712	-0.0505	-0.0349	0.1062	0.0347	0.1166	-27.6432	6.256	-24.3654
15	0.7468	0.9123	-0.5589	2.4736	-1.6867	2.7128	0.0441	-0.0466	-0.0021	-0.1138	-0.0313	0.0182	0.2151	-0.0207	-0.0104	0.1286	-0.0063	0.0059	0.0858	0.0079	0.0848	-23.5329	18.8752	-40.5873
16	2.4538	1.9556	-2.4899	3.0528	-2.0914	4.1226	-0.1735	0.0679	-0.2419	-0.7204	0	-0.1239	0.7611	0.0705	0.1773	0.3085	0.0107	0.0363	0.125	-0.0021	0.1399	-19.895	11.7836	-45.7978
17	3.6757	3.4844	-1.7673	3.52	-1.051	5.4814	-0.0322	0.2743	-0.1511	-0.2647	0.1598	-0.1561	-0.25	-0.5251	-0.099	0.148	0.0497	0.0257	0.1535	0.0143	0.3229	-25.1975	44.4551	-15.2878
18	3.2562	2.7766	-4.0231	3.1718	-2.771	5.488	-0.1499	0.3317	0.4272	-0.081	0.1881	0.4393	-0.0853	-0.789	0.146	0.1193	0.0045	0.0065	0.1724	0.0008	0.1974	-26.4935	39.5537	-14.5734
19	3.7013	0.8241	-1.4539	3.876	0.1372	2.6854	0.1115	-0.3899	0.454	0.1216	-0.0343	0.0223	-0.371	-0.2288	-0.0679	0.1826	0.0533	0.014	0.1887	-0.0762	0.1914	-25.635	45.5377	-6.9186
20	5.3572	3.8921	1.4078	5.1791	0.3278	3.9906	0.0449	-0.1228	0.2953	-0.0805	0.194	-0.1095	-0.5111	-0.1465	-0.1913	0.2644	0.0647	0.0942	0.1455	-0.0386	0.2925	-25.2759	49.4564	-12.4407
21	6.1544	-0.9478	4.8694	3.6971	-0.0121	6.7605	0.1683	-0.2669	0.029	0.4778	-0.1776	-0.3795	0.2657	0.4369	0.0138	0.2202	-0.0116	-0.0113	0.1997	0.0423	0.15	-24.1768	-13.9329	1.8572
22	5.0535	3.7474	1.3282	3.5375	0.9042	2.4845	0.2217	-0.0724	-0.1863	0.2997	-0.1396	-0.0736	0.056	0.0958	-0.091	0.1115	0.0046	-0.0076	0.0586	0.0263	0.1009	-27.6179	-8.5643	-7.5756
23	3.6698	0.9338	4.7302	3.6127	1.1793	6.6147	0.3063	-0.3276	0.1341	0.539	-0.3377	0.3871	-0.1608	0.0324	0.0364	0.2317	-0.0559	0.0587	0.1628	0.0011	0.1214	-31.9618	-3.6266	-1.568
24	4.7333	-2.1919	-1.3788	4.0735	1.7526	3.9018	0.0327	0.2124	-0.0216	-0.2034	-0.0587	0.2454	0.0426	-0.3222	0.0484	0.1683	-0.0322	-0.0574	0.1276	0.0119	0.1479	-24.9869	21.9179	-21.6862

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 128 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 129 through 150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151 through 174 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 175 through 188 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 189 through 214 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 18 through 32 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 33 through 52 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 53 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 110 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 111 through 126 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 127 through 195 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 196 through 223 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 19 through 33 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 34 through 42 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 43 through 72 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 73 through 81 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 16 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 17 through 35 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 36 through 54 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 0 through 13 )

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Antibody , 3 types, 3 molecules ABC

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Protein / Protein/peptide , 2 types, 2 molecules ED

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Non-polymers , 2 types, 858 molecules

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Experimental details

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Experiment

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Sample preparation

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Processing

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-Antibody , 3 types, 3 molecules ABC

-Protein / Protein/peptide , 2 types, 2 molecules ED

-Non-polymers , 2 types, 858 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 3 types, 3 molecules ABC

-
Protein / Protein/peptide , 2 types, 2 molecules ED

-
Non-polymers , 2 types, 858 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi