MolNFT v1 · #123321 · protein
Crystal structure of MAPE1
5JGF · Vacuolar aminopeptidase 1: “Crystal structure of MAPE1”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #123321 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JGF
- Type
- protein
- Length
- 1,842 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
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 460 | 32% helix, 23% strand | P14904 |
| D | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 462 | 32% helix, 24% strand | P14904 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.83 | 0.95 | 37 | empty |
| 2 | 316 | 0.64 | 0.80 | 57 | empty |
| 3 | 67 | 0.62 | 0.92 | 24 | empty |
| 4 | 95 | 0.59 | 0.87 | 30 | empty |
| 5 | 147 | 0.55 | 0.81 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3280 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3242 Ų buried · 58 hydrogen bonds · protein-protein
- B–D · 1758 Ų buried · 31 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 5JGF · PDBe 5JGF · UniProt P14904
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