MolNFT v1 · #142839 · protein
D45W/H226G mutant of marine bacterial prolidase
6AH7 · Xaa-pro dipeptidase: “D45W/H226G mutant of marine bacterial prolidase”. X-ray diffraction, 3 ligands (MN, NA, SO4), 19 pockets (best druggability 0.83). MolNFT v1 #142839 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AH7
- 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, NA, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% 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 | 38% helix, 17% strand | A0A1I7CHQ2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.83 | 0.85 | 93 | empty |
| 2 | 1118 | 0.82 | 0.83 | 105 | empty |
| 3 | 970 | 0.80 | 0.82 | 96 | empty |
| 4 | 52 | 0.73 | 0.99 | 18 | empty |
| 5 | 62 | 0.72 | 0.98 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2386 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2381 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AH7 · D45W/H226G mutant of marine bacterial prolidase · the same entry in another collection · chain B against B, 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 6AH7 · PDBe 6AH7 · UniProt A0A1I7CHQ2
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