Research workbench
Human methionine aminopeptidase in complex with bengamide inhibitor LAF153 and cobalt
Analyse Human methionine aminopeptidase in complex with bengamide inhibitor LAF153 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QZY
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 2
- EC
- 3.4.11.18
- UniProt
- P50579
- Ligands
- TDE, CO
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 355 | 32% helix, 26% strand | P50579 |
Ligands and binding sites
- TDE · (E)-(2R,3R,4S,5R)-3,4,5-trihydroxy-2-methoxy-8,8-dimethyl-non-6-enoic acid ((3S,6R)-6-hydroxy-2-oxo-azepan-3-yl)-amide · ligand · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A
- TBU · Tertiary-butyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.69 | 0.87 | 33 | TDE |
| 2 | 66 | 0.49 | 0.85 | 17 | empty |
| 3 | 52 | 0.24 | 0.72 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1QZY · Human Methionine Aminopeptidase in complex with bengamide inhibitor LAF153 and cobalt · 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 1QZY · PDBe 1QZY · UniProt P50579
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