Research workbench
Human methionine aminopeptidase type 1B (F309M mutant) in complex with ovalicin
Analyse Human methionine aminopeptidase type 1B (F309M mutant) in complex with ovalicin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKP
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 1
- EC
- 3.4.11.18
- UniProt
- P53582
- Ligands
- OVA, CO, K
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 1 (EC 3.4.11.18) | protein | 305 | 27% helix, 22% strand | P53582 |
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 · 3 copies · chains A
- K · Potassium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.64 | 0.94 | 20 | empty |
| 2 | 244 | 0.63 | 0.81 | 34 | OVA |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5YKP · Human methionine aminopeptidase type 1b (F309M mutant) in complex with ovalicin · the same entry in another collection · chain A against A, TM-score 1.00
- P53582 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase 1 (P53582) · 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 P53582
- Elsewhere: RCSB PDB 5YKP · PDBe 5YKP · UniProt P53582
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