Download MendeleyCrystal Structure Of I83E Meditope-Enabled Trastuzumab With Azido-Meditope
Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.To be published.
5U5M
CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-MEDITOPE
- PDB DOI: https://doi.org/10.2210/pdb5U5M/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Finegoldia magna, Staphylococcus aureus, synthetic construct
- Expression System: Cricetulus griseus, Escherichia coli
- Mutation(s): Yes
- Deposited: 2016-12-06 Released: 2018-03-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 ?
- R-Value Free: 0.197
- R-Value Work: 0.161
- R-Value Observed: 0.163
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MEMAB TRASTUZUMAB, LIGHT CHAIN | 214 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MEMAB TRASTUZUMAB, HEAVY CHAIN | 223 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protein L | C [auth E] | 63 | Finegoldia magna | Mutation(s): 5 |  |
UniProt | |||||
Find proteins for Q51918 (Finegoldia magna) Explore Q51918 Go to UniProtKB: Q51918 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q51918 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Immunoglobulin G binding protein A | D [auth C] | 54 | Staphylococcus aureus | Mutation(s): 0 Gene Names: spa |  |
UniProt | |||||
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976 Go to UniProtKB: P02976 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02976 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| AZIDO-PEG4-MEDITOPE | E [auth D] | 13 | synthetic construct | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MRY Query on MRY | F [auth B] | MESO-ERYTHRITOL C4 H10 O4 UNXHWFMMPAWVPI-ZXZARUISSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 2GX Query on 2GX | E [auth D] | L-PEPTIDE LINKING | C15 H15 N O2 |  | PHE |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 ?
- R-Value Free: 0.197
- R-Value Work: 0.161
- R-Value Observed: 0.163
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 53.53 | ¦Á = 90 |
| b = 105.47 | ¦Â = 90 |
| c = 117.13 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
Entry History
Deposition Data
- Released Date: 2018-03-14 Deposition Author(s): Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.
Revision History (Full details and data files)
- Version 1.0: 2018-03-14
Type: Initial release - Version 1.1: 2018-03-28
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary - Version 1.2: 2018-04-18
Changes: Data collection - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description - Version 1.4: 2023-11-15
Changes: Data collection, Derived calculations
