4KRP
Nanobody/VHH domain 9G8 in complex with the extracellular region of EGFR
- PDB DOI: https://doi.org/10.2210/pdb4KRP/pdb
- Classification: TRANSFERASE/IMMUNE SYSTEM
- Organism(s): Homo sapiens, Lama glama, Mus musculus
- Expression System: Spodoptera frugiperda, Escherichia coli, Mus musculus
- Mutation(s): No
- Deposited: 2013-05-16 Released: 2013-08-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.82 Å
- R-Value Free: 0.263
- R-Value Work: 0.215
- R-Value Observed: 0.217
This is version 2.1 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 |
| Epidermal growth factor receptor | 625 | Homo sapiens | Mutation(s): 0 Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00533 (Homo sapiens) Explore P00533 Go to UniProtKB: P00533 | |||||
PHAROS: P00533 GTEx: ENSG00000146648 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00533 | ||||
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 |
| Nanobody/VHH domain 9G8 | 136 | Lama glama | 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: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cetuximab light chain | 211 | 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: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cetuximab 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 | |||||
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Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | G [auth A], H [auth A], I [auth A], J [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.82 Å
- R-Value Free: 0.263
- R-Value Work: 0.215
- R-Value Observed: 0.217
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.372 | α = 90 |
| b = 95.841 | β = 99.95 |
| c = 129.481 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| JBluIce-EPICS | data collection |
| HKL-3000 | data reduction |
Entry History
Deposition Data
- Released Date: 2013-08-28 Deposition Author(s): Ferguson, K.M., Schmitz, K.R.
Revision History (Full details and data files)
- Version 1.0: 2013-08-28
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
