MolNFT v1 · #51325 · protein
GLU383ALA escherichia COLI aminopeptidase P in complex with substrate
2V3Z · Xaa-pro aminopeptidase: “GLU383ALA escherichia COLI aminopeptidase P in complex with substrate”. X-ray diffraction, 2 ligands (MN, CL), 3 pockets (best druggability 0.53). MolNFT v1 #51325 on GenesisL1: 3D structure, binding sites…
- PDB
- 2V3Z
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro aminopeptidase; Tripeptide (valine-proline-leucine)
- EC
- 3.4.11.9
- UniProt
- P15034
- Ligands
- MN, CL
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 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 | 42% helix, 19% strand | P15034 |
| B | Tripeptide (valine-proline-leucine) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.53 | 0.75 | 36 | empty |
| 2 | 71 | 0.33 | 0.75 | 16 | empty |
| 3 | 62 | 0.27 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 2V3Z · Glu383Ala Escherichia coli aminopeptidase P in complex with substrate · the same entry in another collection · chain A against A, TM-score 1.00
- P15034 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase (P15034) · a predicted model of the same protein · 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 P15034
- Elsewhere: RCSB PDB 2V3Z · PDBe 2V3Z · UniProt P15034
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