Research workbench
The product bound form of the MN(II)LOADED methionine aminopeptidase from hyperthermophile pyrococcus furiosus
Analyse The product bound form of the MN(II)LOADED methionine aminopeptidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WKM
- 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
- MET, MN
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 295 | 32% helix, 28% strand | P56218 |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
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 | 197 | 0.60 | 0.82 | 34 | MET |
| 2 | 168 | 0.60 | 0.83 | 30 | MET |
| 3 | 98 | 0.36 | 0.74 | 25 | empty |
| 4 | 106 | 0.35 | 0.73 | 19 | empty |
| 5 | 81 | 0.33 | 0.74 | 16 | empty |
Compared structures
- 1WKM · The product bound form of the MN(II)LOADED methionine aminopeptidase from… · 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 B 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 1WKM · PDBe 1WKM · UniProt P56218
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