MolNFT v1 · #141732 · protein
Structure of vanyb unbound
5ZHF · D-alanyl-D-alanine carboxypeptidase: “Structure of vanyb unbound”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.75). MolNFT v1 #141732 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZHF
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- Q47746
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 181 | 48% helix, 14% strand | Q47746 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.75 | 0.79 | 92 | ZN, PG4 |
| 2 | 94 | 0.44 | 0.80 | 19 | empty |
| 3 | 67 | 0.44 | 0.82 | 17 | empty |
| 4 | 99 | 0.44 | 0.79 | 19 | GOL |
| 5 | 84 | 0.44 | 0.80 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
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 Q47746
- Elsewhere: RCSB PDB 5ZHF · PDBe 5ZHF · UniProt Q47746
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