MolNFT v1 · #102059 · protein
Crystal structure of vancomycin resistance D,D-DIPEPTIDASE/D,D- pentapeptidase vanxyc D59S mutant in complex with D-alanine-D-alanine and copper (II)
4OAK · D,D-DIPEPTIDASE/D,D-carboxypeptidase: “Crystal structure of vancomycin resistance D,D-DIPEPTIDASE/D,D- pentapeptidase vanxyc D59S mutant in complex…”. X-ray diffraction, 4 ligands (CU, MG, CL), 9 pockets (best druggability 0.66).…
- PDB
- 4OAK
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D,D-DIPEPTIDASE/D,D-carboxypeptidase
- UniProt
- Q9JN36
- Ligands
- CU, MG, CL, SO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D,D-DIPEPTIDASE/D,D-carboxypeptidase | protein | 192 | 40% helix, 14% strand | Q9JN36 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.66 | 0.95 | 16 | empty |
| 2 | 147 | 0.45 | 0.76 | 26 | CL, SO4 |
| 3 | 70 | 0.43 | 0.81 | 17 | empty |
| 4 | 83 | 0.42 | 0.79 | 17 | empty |
| 5 | 98 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino (D-amino acid).
Compared structures
- 4OAK · Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S… · 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 Q9JN36
- Elsewhere: RCSB PDB 4OAK · PDBe 4OAK · UniProt Q9JN36
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.