MolNFT v1 · #142840 · protein
Marine bacterial prolidase with promiscuous organophosphorus hydrolase activity
6AH8 · Xaa-pro dipeptidase: “Marine bacterial prolidase with promiscuous organophosphorus hydrolase activity”. X-ray diffraction, 2 ligands (MN, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #142840 on GenesisL1: 3D structure…
- PDB
- 6AH8
- Type
- protein
- Length
- 1,756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidase
- EC
- 3.4.13.9
- UniProt
- A0A1I7CHQ2
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 439 | 39% helix, 17% strand | A0A1I7CHQ2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.85 | 0.86 | 125 | MN |
| 2 | 489 | 0.81 | 0.88 | 60 | empty |
| 3 | 335 | 0.77 | 0.88 | 48 | empty |
| 4 | 593 | 0.63 | 0.74 | 45 | SO4 |
| 5 | 178 | 0.45 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2385 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2381 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6AH8 · Marine bacterial prolidase with promiscuous organophosphorus hydrolase activity · 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 A0A1I7CHQ2
- Elsewhere: RCSB PDB 6AH8 · PDBe 6AH8 · UniProt A0A1I7CHQ2
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