MolNFT v1 · #60118 · protein
Crystal structure of cold-aminopeptidase from colwellia psychrerythraea
3CIA · Cold-active aminopeptidase: “Crystal structure of cold-aminopeptidase from colwellia psychrerythraea”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #60118 on GenesisL1: 3D structure, binding sites…
- PDB
- 3CIA
- Type
- protein
- Length
- 2,331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cold-active aminopeptidase
- EC
- 3.4.11.-
- UniProt
- Q7WVY1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cold-active aminopeptidase (EC 3.4.11.-) | protein | 587 | 36% helix, 21% strand | Q7WVY1 |
| B, C | Cold-active aminopeptidase (EC 3.4.11.-) | protein | 581 | 36% helix, 21% strand | Q7WVY1 |
| D | Cold-active aminopeptidase (EC 3.4.11.-) | protein | 582 | 37% helix, 21% strand | Q7WVY1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.83 | 0.84 | 62 | ZN |
| 2 | 1084 | 0.83 | 0.84 | 78 | ZN |
| 3 | 1066 | 0.82 | 0.83 | 64 | ZN |
| 4 | 1054 | 0.82 | 0.83 | 67 | ZN |
| 5 | 61 | 0.69 | 0.95 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 109 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 108 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3CIA · Crystal structure of cold-aminopeptidase from Colwellia psychrerythraea · 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 Q7WVY1
- Elsewhere: RCSB PDB 3CIA · PDBe 3CIA · UniProt Q7WVY1
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