Research workbench
Crystal structure of human methionine aminopeptidase-2 in complex; with an inhibitor 6-((R)-2-O-tolyloxymethyl-pyrrolidin-1-yl)-9H- purine
Analyse Crystal structure of human methionine aminopeptidase-2 in complex; with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LYW
- Type
- protein
- Length
- 359 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
- 7BH, MN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 359 | 33% helix, 28% strand | P50579 |
Ligands and binding sites
- 7BH · 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine · ligand · chains A
- MN · Manganese (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 | 228 | 0.69 | 0.86 | 35 | 7BH |
| 2 | 61 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 5LYW · CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR… · 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 5LYW · PDBe 5LYW · UniProt P50579
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.