MolNFT v1 · #27172 · protein
Streptomyces griseus aminopeptidase complexed with P-iodo-D- phenylalanine
1XBU: “Streptomyces griseus aminopeptidase complexed with P-iodo-D- phenylalanine”. X-ray diffraction, 3 ligands (IOY, ZN, CA), 1 pocket (best druggability 0.48). MolNFT v1 #27172 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XBU
- Type
- protein
- Length
- 275 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase
- EC
- 3.4.11.-
- UniProt
- P80561
- Ligands
- IOY, ZN, CA
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase (EC 3.4.11.-) | protein | 275 | 42% helix, 20% strand | P80561 |
Ligands and binding sites
- IOY · P-iodo-D-phenylalanine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.48 | 0.81 | 18 | ZN, IOY |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1XBU · Streptomyces griseus aminopeptidase complexed with p-iodo-D-phenylalanine · the same entry in another collection · chain A against A, TM-score 1.00
- P80561 · AlphaFold monomer V2.0 prediction for aminopeptidase S (P80561) · 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 P80561
- Elsewhere: RCSB PDB 1XBU · PDBe 1XBU · UniProt P80561
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