MolNFT v1 · #38329 · protein
Structural basis of catalysis by mononuclear methionine aminopeptidase
2GTX: “Structural basis of catalysis by mononuclear methionine aminopeptidase”. X-ray diffraction, 3 ligands (NLP, MN, NA), 6 pockets (best druggability 0.61). MolNFT v1 #38329 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GTX
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- P0AE18
- Ligands
- NLP, MN, NA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 261 | 28% helix, 28% strand | P0AE18 |
Ligands and binding sites
- NLP · (1-amino-pentyl)-phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 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 | 320 | 0.61 | 0.78 | 42 | NLP |
| 2 | 133 | 0.57 | 0.83 | 27 | NLP |
| 3 | 80 | 0.38 | 0.77 | 15 | empty |
| 4 | 67 | 0.35 | 0.77 | 17 | empty |
| 5 | 82 | 0.35 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2GTX · Structural Basis of Catalysis by Mononuclear Methionine Aminopeptidase · the same entry in another collection · chain A against A, TM-score 1.00
- P0AE18 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase (P0AE18) · a predicted model of the same protein · chain A 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 P0AE18
- Elsewhere: RCSB PDB 2GTX · PDBe 2GTX · UniProt P0AE18
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