1N8Z
Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab
- PDB DOI: https://doi.org/10.2210/pdb1N8Z/pdb
- Classification: TRANSFERASE
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No
- Deposited: 2002-11-21 Released: 2003-02-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.52 Å
- R-Value Free: 0.284
- R-Value Work: 0.222
- R-Value Observed: 0.225
This is version 1.5 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Herceptin Fab (antibody) - light chain | 214 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Herceptin Fab (antibody) - heavy chain | 220 | Mus musculus, Homo sapiens This entity is chimeric | 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 |
| Receptor protein-tyrosine kinase erbB-2 | 607 | Homo sapiens | Mutation(s): 0 Gene Names: HER2(erbB2) EC: 2.7.1.112 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04626 (Homo sapiens) Explore P04626 Go to UniProtKB: P04626 | |||||
PHAROS: P04626 GTEx: ENSG00000141736 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04626 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth C], E [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | F [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.52 Å
- R-Value Free: 0.284
- R-Value Work: 0.222
- R-Value Observed: 0.225
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.17 | α = 90 |
| b = 109.77 | β = 90 |
| c = 175.14 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
Entry History
Deposition Data
- Released Date: 2003-02-18 Deposition Author(s): Cho, H.-S., Mason, K., Ramyar, K.X., Stanley, A.M., Gabelli, S.B., Denney Jr., D.W., Leahy, D.J.
Revision History (Full details and data files)
- Version 1.0: 2003-02-18
Type: Initial release - Version 1.1: 2008-05-05
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2014-02-05
Changes: Source and taxonomy - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary
