Research workbench
Znmg substituted aminopeptidase P from E. COLI
Analyse Znmg substituted aminopeptidase P from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7V
- Type
- protein
- Length
- 1,765 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro aminopeptidase; Peptide val-pro-leu
- EC
- 3.4.11.9
- UniProt
- P15034
- Ligands
- MG, ZN, CL
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro aminopeptidase (EC 3.4.11.9) | protein | 440 | 41% helix, 18% strand | P15034 |
| B, C, D | Xaa-pro aminopeptidase (EC 3.4.11.9) | protein | 439 | 41% helix, 19% strand | P15034 |
| E, F, G, H | Peptide val-pro-leu | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, G, D, H
- ZN · Zinc ion · metal · 4 copies · chains A, B, F, C, G, D, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.83 | 0.93 | 42 | empty |
| 2 | 913 | 0.77 | 0.80 | 63 | empty |
| 3 | 922 | 0.76 | 0.79 | 65 | empty |
| 4 | 1036 | 0.76 | 0.78 | 87 | empty |
| 5 | 556 | 0.64 | 0.76 | 64 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2161 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 657 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 280 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 278 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
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 P15034
- Elsewhere: RCSB PDB 1W7V · PDBe 1W7V · UniProt P15034
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