MolNFT v1 · #104439 · protein
Crystal structure of an engineered lipocalin (anticalin) in complex with VEGF(8-109)
4QAF · Lipocalin-1: “Crystal structure of an engineered lipocalin (anticalin) in complex with VEGF(8-109)”. X-ray diffraction, 2 ligands (OMA, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #104439 on GenesisL1: 3D structure, binding…
- PDB
- 4QAF
- Type
- protein
- Length
- 389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipocalin-1; Vascular endothelial growth factor a
- UniProt
- P31025, P15692
- Ligands
- OMA, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipocalin-1 | protein | 109 | 3% helix, 45% strand | P31025 |
| C | Vascular endothelial growth factor a | protein | 96 | 16% helix, 63% strand | P15692 |
| D | Vascular endothelial growth factor a | protein | 95 | 13% helix, 61% strand | P15692 |
| B | Lipocalin-1 | protein | 89 | 3% helix, 48% strand | P31025 |
Ligands and binding sites
- OMA · 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains C, B, A, D
- ACT · Acetate ion · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.76 | 0.91 | 25 | OMA |
| 2 | 387 | 0.73 | 0.84 | 49 | OMA, ACT |
| 3 | 120 | 0.40 | 0.75 | 22 | empty |
| 4 | 62 | 0.32 | 0.76 | 16 | empty |
| 5 | 57 | 0.27 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1375 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 499 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4QAF · Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109) · the same entry in another collection · chain A against A, TM-score 1.00
- P31025 · AlphaFold monomer V2.0 prediction for lipocalin-1 (P31025) · a predicted model of the same protein · chain A against A, TM-score 0.53
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P31025
- Every structure of UniProt P15692
- Elsewhere: RCSB PDB 4QAF · PDBe 4QAF · UniProt P31025 · UniProt P15692
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