MolNFT v1 · #177031 · protein
Bacterial prolidase mutant D45W/L225Y/H226L/H343I
7E5C · Xaa-pro dipeptidase: “Bacterial prolidase mutant D45W/L225Y/H226L/H343I”. X-ray diffraction, 1 ligand (MN), 16 pockets (best druggability 0.84). MolNFT v1 #177031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E5C
- Type
- protein
- Length
- 1,755 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
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 439 | 39% helix, 18% strand | A0A1I7CHQ2 |
| D | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 438 | 39% helix, 18% strand | A0A1I7CHQ2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.84 | 0.88 | 96 | empty |
| 2 | 539 | 0.82 | 0.88 | 81 | empty |
| 3 | 233 | 0.70 | 0.86 | 40 | MN |
| 4 | 191 | 0.68 | 0.86 | 29 | empty |
| 5 | 182 | 0.66 | 0.86 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2537 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2487 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7E5C · Bacterial prolidase mutant D45W/L225Y/H226L/H343I · 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 7E5C · PDBe 7E5C · UniProt A0A1I7CHQ2
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