MolNFT v1 · #155743 · protein
Crystal structure of vibrio cholerae methionine aminopeptidase with partially occupied metals
6LH7: “Crystal structure of vibrio cholerae methionine aminopeptidase with partially occupied metals”. X-ray diffraction, 2 ligands (NI, NA), 5 pockets (best druggability 0.58). MolNFT v1 #155743 on GenesisL1: 3D structure, binding sites…
- PDB
- 6LH7
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- Q9KPV1
- Ligands
- NI, NA
- Pockets
- 5 · best druggability 0.58
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 | 279 | 28% helix, 28% strand | Q9KPV1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.58 | 0.84 | 23 | NI |
| 2 | 119 | 0.57 | 0.84 | 21 | empty |
| 3 | 251 | 0.46 | 0.73 | 32 | empty |
| 4 | 187 | 0.42 | 0.73 | 29 | empty |
| 5 | 53 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LH7 · Crystal Structure of Vibrio cholerae Methionine Aminopeptidase with Partially Occupied… · the same entry in another collection · 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 Q9KPV1
- Elsewhere: RCSB PDB 6LH7 · PDBe 6LH7 · UniProt Q9KPV1
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