Download MendeleyCrystal structure of an Anticalin with specific blocking activity towards human vascular endothelial growth factor (VEGF) reveals plasticity of the lipocalin fold
Giese, T., Skerra, A.To be published.
4QAF
Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
- PDB DOI: https://doi.org/10.2210/pdb4QAF/pdb
- Classification: TRANSPORT PROTEIN/SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli, Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2014-05-04 Released: 2015-05-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242
- R-Value Work: 0.203
- R-Value Observed: 0.205
This is version 1.1 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 |
| Lipocalin-1 | A, D [auth B] | 152 | Homo sapiens | Mutation(s): 27 Gene Names: engineered variant, LCN1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P31025 (Homo sapiens) Explore P31025 Go to UniProtKB: P31025 | |||||
PHAROS: P31025 GTEx: ENSG00000160349 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P31025 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Vascular endothelial growth factor A | B [auth C], C [auth D] | 112 | Homo sapiens | Mutation(s): 0 Gene Names: VEGFA, VEGF |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15692 (Homo sapiens) Explore P15692 Go to UniProtKB: P15692 | |||||
PHAROS: P15692 GTEx: ENSG00000112715 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P15692 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OMA Query on OMA | E [auth A], J [auth B] | 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid C19 H34 O2 MGOIQHKBDDJUJK-XVSUHRFUSA-N |  | ||
| SO4 Query on SO4 | F [auth C], G [auth C], H [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACT Query on ACT | I [auth D] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242
- R-Value Work: 0.203
- R-Value Observed: 0.205
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.21 | α = 90 |
| b = 88.21 | β = 90 |
| c = 103.421 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345dtb | data collection |
| XDS | data reduction |
| Auto-Rickshaw | phasing |
Entry History
Deposition Data
- Released Date: 2015-05-06 Deposition Author(s): Giese, T., Skerra, A.
Revision History (Full details and data files)
- Version 1.0: 2015-05-06
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
