MolNFT v1 · #115578 · protein
Crystal structure of xaa-pro aminopeptidase from escherichia COLI K12
5CNX · Aminopeptidase ypdf: “Crystal structure of xaa-pro aminopeptidase from escherichia COLI K12”. X-ray diffraction, 2 ligands (ZN, NA), 8 pockets (best druggability 0.80). MolNFT v1 #115578 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CNX
- Type
- protein
- Length
- 1,080 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase ypdf
- EC
- 3.4.11.-
- UniProt
- P76524
- Ligands
- ZN, NA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aminopeptidase ypdf (EC 3.4.11.-) | protein | 360 | 36% helix, 24% strand | P76524 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- CAC · Cacodylate ion · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.80 | 0.84 | 101 | CAC |
| 2 | 487 | 0.63 | 0.76 | 46 | empty |
| 3 | 103 | 0.57 | 0.85 | 22 | empty |
| 4 | 90 | 0.51 | 0.83 | 20 | CAC |
| 5 | 101 | 0.45 | 0.79 | 21 | CAC |
Interfaces
2 interfaces between chains.
- A–C · 1484 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 171 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CNX · Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12 · the same entry in another collection · chain A against A, TM-score 1.00
- P76524 · AlphaFold monomer V2.0 prediction for aminopeptidase ypdf (P76524) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P76524
- Elsewhere: RCSB PDB 5CNX · PDBe 5CNX · UniProt P76524
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