PDB-5u5m: CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO...

ID or keywords:

Entry

Database: PDB / ID: 5u5m

Title

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

Components

(MEMAB TRASTUZUMAB, ...) x 2
AZIDO-PEG4-MEDITOPE
Immunoglobulin G binding protein A
Protein L

Keywords

IMMUNE SYSTEM / ANTIBODY / ANTIBODY-DRUG CONJUGATES

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)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.88 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-Meditope
Authors: Williams, J.C. / Bzymek, K.P. / Pucket, J. / Avery, K.A. / Ma, Y. / Xie, J. / Zer, C. / Horne, D.

History

Deposition	Dec 6, 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 / 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 / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _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
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	5u5m.cif.gz	257.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5u5m.ent.gz	206.2 KB	Display	PDB format
PDBx/mmJSON format	5u5m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5u5m_validation.pdf.gz	467 KB	Display	wwPDB validaton report
Full document	5u5m_full_validation.pdf.gz	471.3 KB	Display
Data in XML	5u5m_validation.xml.gz	31 KB	Display
Data in CIF	5u5m_validation.cif.gz	47.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u5/5u5m ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u5m	HTTPS FTP

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Related structure data

Related structure data	4ioiS 5u3d 5u5f 5u6a S: Starting model for refinement
Similar structure data	4q47-1 4ioi-d 6bah-d 4hkz-d 4bj5-1 6bae-d 5u6a-d 4bj6-2 3zgq-d 4bj5-2 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, LIGHT CHAIN

B: MEMAB TRASTUZUMAB, HEAVY CHAIN

E: Protein L

C: Immunoglobulin G binding protein A

D: AZIDO-PEG4-MEDITOPE

hetero molecules

62.1 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.530, 105.470, 117.130
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	MEMAB TRASTUZUMAB, 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	MEMAB TRASTUZUMAB, 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	AZIDO-PEG4-MEDITOPE Mass: 1838.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 733 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.: 732 / 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: 2.67 Å³/Da / Density % sol: 53.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 18 % PEG 3350, 150 MM NACL, 100 MM TRIS, PH 7.2, 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: Apr 13, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.88→31.62 Å / Num. obs: 54740 / % possible obs: 99.9 % / Redundancy: 5.2 % / R_merge(I) obs: 0.1 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.88→1.93 Å / Redundancy: 5 % / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 2.12 / Num. unique all: 3989 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.9_1692	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IOI

4ioi

Resolution: 1.88→31.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7

	R_factor	Num. reflection	% reflection
R_free	0.197	2736	5 %
R_work	0.161	-	-
obs	0.163	54735	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.88→31.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4353	0	8	732	5093

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4607
X-RAY DIFFRACTION	f_angle_d	1.082	6266
X-RAY DIFFRACTION	f_dihedral_angle_d	14.375	1712
X-RAY DIFFRACTION	f_chiral_restr	0.044	694
X-RAY DIFFRACTION	f_plane_restr	0.005	818

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 (%)
1.8799-1.9123	0.326	135	0.2496	2577	X-RAY DIFFRACTION	100
1.9123-1.9471	0.2742	133	0.2248	2518	X-RAY DIFFRACTION	100
1.9471-1.9845	0.254	137	0.2087	2610	X-RAY DIFFRACTION	100
1.9845-2.025	0.2286	133	0.1878	2531	X-RAY DIFFRACTION	100
2.025-2.069	0.2453	136	0.1875	2569	X-RAY DIFFRACTION	100
2.069-2.1171	0.2075	135	0.182	2583	X-RAY DIFFRACTION	100
2.1171-2.1701	0.1876	135	0.1764	2549	X-RAY DIFFRACTION	100
2.1701-2.2287	0.2155	136	0.1656	2596	X-RAY DIFFRACTION	100
2.2287-2.2943	0.2117	135	0.1741	2560	X-RAY DIFFRACTION	100
2.2943-2.3683	0.1923	136	0.1626	2577	X-RAY DIFFRACTION	100
2.3683-2.4529	0.2192	136	0.1724	2592	X-RAY DIFFRACTION	100
2.4529-2.5511	0.2214	137	0.171	2601	X-RAY DIFFRACTION	100
2.5511-2.6672	0.2359	135	0.1678	2572	X-RAY DIFFRACTION	100
2.6672-2.8077	0.2178	138	0.1684	2610	X-RAY DIFFRACTION	100
2.8077-2.9835	0.2006	137	0.1627	2609	X-RAY DIFFRACTION	100
2.9835-3.2136	0.1909	137	0.1586	2609	X-RAY DIFFRACTION	100
3.2136-3.5367	0.1662	138	0.1458	2622	X-RAY DIFFRACTION	100
3.5367-4.0475	0.1688	139	0.1378	2643	X-RAY DIFFRACTION	100
4.0475-5.096	0.1357	141	0.1165	2670	X-RAY DIFFRACTION	100
5.096-31.6252	0.1955	147	0.1651	2801	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	1.1897	-0.6192	-0.6888	2.8424	-3.2292	5.4357	0.047	0.0491	0.0019	0.0739	0.1382	-0.008	-0.2731	-0.1443	-0.2347	0.1625	-0.0076	0.0015	0.1524	-0.0333	0.1878	-18.9479	34.9254	-10.2985
2	1.9121	0.476	0.3621	1.7309	-0.606	0.3674	0.0049	-0.0974	0.069	-0.0263	0.0138	-0.2395	-0.1221	0.2058	-0.0255	0.1015	-0.0131	0.0026	0.1585	-0.0184	0.169	-10.3886	28.4416	-8.3089
3	0.1813	-0.288	0.2817	0.4055	-0.6622	1.6143	0.0325	0.0268	-0.0029	-0.091	0.0482	0.0258	0.1066	-0.0246	-0.0549	0.1299	-0.0327	-0.0007	0.1136	0.0013	0.1104	-21.0035	26.6722	-24.7532
4	2.5607	1.5458	1.0598	2.7856	0.6734	2.8695	0.0964	-0.119	-0.0578	-0.0075	0.0349	0.0764	0.0763	-0.253	-0.1143	0.1442	-0.0131	0.0034	0.1333	0.0348	0.1128	-30.6606	30.2998	-37.0147
5	4.0735	2.0889	2.1485	2.0862	1.5813	3.005	0.0646	-0.0412	-0.0667	-0.2948	0.0414	0.5171	0.4139	-0.5371	0.0033	0.3303	-0.1327	-0.1437	0.2928	0.0639	0.3003	-40.3581	20.2226	-45.1015
6	3.0809	2.9138	2.4993	5.7912	2.9684	3.8284	-0.0938	0.1807	0.0054	-0.3517	0.2521	0.321	0.1699	-0.1257	-0.1229	0.209	-0.0338	-0.0631	0.1775	0.0407	0.1672	-35.4913	32.834	-47.6569
7	0.8917	-0.1725	0.7114	1.7703	-0.0938	2.0174	-0.1811	0.274	0.2135	-0.3985	0.2161	0.0176	0.1112	0.1342	-0.0452	0.197	-0.0149	0.0011	0.1452	-0.0132	0.1371	-19.3331	4.4846	-18.0275
8	3.8305	2.6157	-0.2914	2.7424	1.0056	1.5207	-0.0652	-0.1974	-0.1566	-0.0506	0.1032	-0.4002	0.1187	0.3122	-0.0328	0.0967	0.0431	-0.0021	0.1704	0.0044	0.2324	-7.9219	4.0115	-11.097
9	2.3765	-1.1755	1.0612	3.1935	-1.7561	2.8594	0.0431	-0.2031	0.0184	0.1147	0.0374	0.0443	-0.049	0.0219	-0.0775	0.1154	-0.0356	-0.0071	0.136	-0.0074	0.1258	-18.5645	12.2973	-7.6255
10	7.4868	-1.1268	2.0151	2.1541	0.0513	2.5854	-0.0627	-0.4648	0.1125	0.2388	-0.0306	-0.1655	0.0344	-0.1806	0.0798	0.2222	-0.0373	-0.0092	0.1858	0.0168	0.1615	-19.3564	5.2563	-0.23
11	2.0585	1.5441	0.8112	1.7539	-0.5734	2.6721	0.0642	-0.0302	-0.2682	-0.0003	0.0558	-0.0936	0.06	-0.0107	-0.1207	0.1548	-0.0113	-0.008	0.0973	-0.0099	0.1375	-19.2321	1.7252	-10.2838
12	4.6095	1.0693	1.0915	2.2037	0.407	2.7298	-0.003	-0.2919	0.1245	-0.0415	-0.0057	-0.4035	-0.1174	0.3162	0.0329	0.1383	-0.0122	0.0155	0.1948	-0.0084	0.2368	-9.6739	14.8625	-9.4903
13	0.2199	-0.1147	0.1554	0.9807	-1.5514	2.4056	0.0373	0.0466	-0.0074	-0.3439	0.1327	0.1185	0.3571	-0.1473	-0.1512	0.2506	-0.0317	-0.0277	0.1305	-0.0021	0.1334	-26.2679	14.6807	-36.5583
14	0.5857	0.865	-0.0448	2.3465	-1.2306	2.5026	0.0482	-0.0432	-0.0447	-0.3166	-0.1081	-0.1247	0.427	0.0654	0.0721	0.2355	0.0151	0.0295	0.136	0.017	0.1494	-21.9251	16.4508	-39.4934
15	4.9526	1.7717	-2.4511	2.0203	0.1438	2.9814	-0.1477	0.6158	-0.2256	-0.8631	0.0542	0.0307	0.3297	-0.3084	0.0739	0.6273	-0.0079	0.039	0.2446	-0.066	0.2127	-22.5212	11.655	-49.1142
16	3.7283	5.0626	-1.79	7.5379	-1.2715	4.4844	0.1698	0.5017	-0.0406	-0.1699	0.0965	-0.0797	-0.3813	-0.4048	-0.2126	0.2056	0.0606	0.0354	0.1942	0.015	0.3947	-25.4828	44.5474	-15.4326
17	5.2445	1.2158	-1.0875	3.0543	0.25	2.6317	-0.0082	-0.5291	0.3852	0.2145	-0.037	0.1124	-0.1857	-0.1635	0.0402	0.1454	0.0505	-0.0048	0.1853	-0.0493	0.1939	-25.3747	41.7177	-8.4718
18	3.7161	3.3406	0.2932	3.3506	-1.0396	4.9297	0.2476	0.3485	0.6194	-0.1972	0.259	0.0528	-0.6742	-0.8688	-0.1331	0.4724	0.1473	0.0857	0.3713	-0.2119	0.5838	-28.9421	51.0623	-10.1286
19	4.251	2.657	2.0919	4.8886	-0.4344	4.613	0.3867	0.0403	0.4228	0.0126	0.3855	0.1069	-0.4904	-0.2704	-0.4367	0.357	0.0648	0.1396	0.1769	-0.0735	0.4103	-25.6123	49.5207	-12.536
20	7.6374	-1.3965	3.3953	1.5698	-0.2398	4.0578	0.3381	-0.7192	-0.179	0.4757	-0.3366	-0.5048	0.278	0.5303	0.0889	0.3506	-0.0635	-0.0412	0.3654	0.0917	0.2949	-24.3989	-13.8526	2.2111
21	2.1917	1.964	0.8107	2.4774	0.5106	2.1613	0.1005	0.0207	-0.1323	0.2413	-0.0537	-0.0542	0.1231	0.0651	-0.0451	0.1797	-0.0001	-0.007	0.1286	0.029	0.1694	-27.7879	-8.6052	-7.5809
22	6.8896	1.3549	4.4931	3.0425	1.2397	4.8334	0.2926	-0.494	0.2458	0.5187	-0.3951	0.3576	0.0219	-0.068	0.05	0.2633	-0.0522	0.0644	0.2052	-0.0002	0.1517	-32.1927	-3.6587	-1.6304
23	4.3315	-0.0604	-0.3147	7.9999	1.827	4.9444	-0.1919	0.226	0.0761	-0.2613	0.1202	0.2208	0.0737	-0.08	0.1401	0.2063	-0.022	-0.0373	0.1601	0.006	0.1123	-23.2547	19.3345	-22.0929

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 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 110 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 111 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 223 )
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 72 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 73 THROUGH 81 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 1 THROUGH 16 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 17 THROUGH 35 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 36 THROUGH 54 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 1 THROUGH 12 )

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Components

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Antibody , 3 types, 3 molecules ABC

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

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Non-polymers , 2 types, 733 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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

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-Assembly

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-Antibody , 3 types, 3 molecules ABC

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

-Non-polymers , 2 types, 733 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, 733 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