MolNFT v1 · #1554 · protein
Complex of human methionine aminopeptidase-2 complexed with ovalicin
1B59 · Protein (methionine aminopeptidase): “Complex of human methionine aminopeptidase-2 complexed with ovalicin”. X-ray diffraction, 2 ligands (OVA, CO), 2 pockets (best druggability 0.68). MolNFT v1 #1554 on GenesisL1: 3D structure…
- PDB
- 1B59
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (methionine aminopeptidase)
- EC
- 3.4.11.18
- UniProt
- P50579
- Ligands
- OVA, CO
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (methionine aminopeptidase) (EC 3.4.11.18) | protein | 355 | 32% helix, 26% strand | P50579 |
Ligands and binding sites
- OVA · 3,4-dihydroxy-2-methoxy-4-methyl-3-[2-methyl-3-(3-methyl-but-2-enyl) -oxiranyl]-cyclohexanone · ligand · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.68 | 0.83 | 39 | OVA |
| 2 | 52 | 0.25 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 1B59 · Complex of human methionine aminopeptidase-2 complexed with ovalicin · the same entry in another collection · chain A against A, TM-score 1.00
- P50579 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase 2 (P50579) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P50579
- Elsewhere: RCSB PDB 1B59 · PDBe 1B59 · UniProt P50579
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