MolNFT v1 · #27333 · protein
Methionine aminopeptidase from hyperthermophile pyrococcus furiosus
1XGM: “Methionine aminopeptidase from hyperthermophile pyrococcus furiosus”. X-ray diffraction, 1 ligand (CO), 10 pockets (best druggability 0.77). MolNFT v1 #27333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XGM
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- P56218
- Ligands
- CO
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 295 | 32% helix, 27% strand | P56218 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.77 | 0.98 | 22 | empty |
| 2 | 71 | 0.69 | 0.95 | 26 | empty |
| 3 | 220 | 0.65 | 0.83 | 39 | empty |
| 4 | 139 | 0.48 | 0.78 | 18 | empty |
| 5 | 136 | 0.43 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1239 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1XGM · Methionine aminopeptidase from hyperthermophile pyrococcus furiosus · the same entry in another collection · chain A against A, TM-score 1.00
- P56218 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase (P56218) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P56218
- Elsewhere: RCSB PDB 1XGM · PDBe 1XGM · UniProt P56218
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