Download MendeleyMeditope Enabled Trastuzumab I83E Variant
Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.To be published.
5U3D
STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT
- PDB DOI: https://doi.org/10.2210/pdb5U3D/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Finegoldia magna, Staphylococcus aureus
- Expression System: Cricetulus griseus, Escherichia coli
- Mutation(s): Yes
- Deposited: 2016-12-01 Released: 2018-03-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.185
- R-Value Work: 0.157
- R-Value Observed: 0.158
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 FAB LIGHT CHAIN I83E | 214 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MEMAB TRASTUZUMAB FAB HEAVY CHAIN | 223 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protein L | C [auth E] | 65 | 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 | |||||
| |||||
Find similar proteins by:
(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 | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MRY Query on MRY | E [auth A] | MESO-ERYTHRITOL C4 H10 O4 UNXHWFMMPAWVPI-ZXZARUISSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.185
- R-Value Work: 0.157
- R-Value Observed: 0.158
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 52.85 | α = 90 |
| b = 104.65 | β = 90 |
| c = 116.88 | γ = 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): Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.
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: 2024-10-30
Changes: Structure summary
