MolNFT v1 · #105559 · protein
Crystal structure of yeast aminopeptidase 1 (APE1)
4R8F · Vacuolar aminopeptidase 1: “Crystal structure of yeast aminopeptidase 1 (APE1)”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #105559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R8F
- Type
- protein
- Length
- 1,735 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar aminopeptidase 1
- EC
- 3.4.11.22
- UniProt
- P14904
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 438 | 32% helix, 26% strand | P14904 |
| B | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 428 | 32% helix, 26% strand | P14904 |
| C | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 437 | 32% helix, 25% strand | P14904 |
| D | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 432 | 31% helix, 27% strand | P14904 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.79 | 0.82 | 58 | empty |
| 2 | 108 | 0.78 | 0.98 | 21 | empty |
| 3 | 95 | 0.76 | 0.97 | 21 | empty |
| 4 | 86 | 0.76 | 0.98 | 22 | empty |
| 5 | 260 | 0.60 | 0.80 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2578 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1922 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1883 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1726 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
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 P14904
- Elsewhere: RCSB PDB 4R8F · PDBe 4R8F · UniProt P14904
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