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 | pdb_00004qaf
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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.203 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.205 (Depositor)
Starting Model: experimental
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This is version 1.2 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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.203 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.205 (Depositor)
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 - Version 1.2: 2024-10-16
Changes: Structure summary
