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Crystal structure of vancomycin resistance D,D-DIPEPTIDASE/D,D- pentapeptidase vanxyc D59S mutant in complex with D-alanine
Analyse Crystal structure of vancomycin resistance D,D-DIPEPTIDASE/D,D- pentapeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MUT
- Type
- protein
- Length
- 375 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
- DAL, ZN, CL, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D,D-DIPEPTIDASE/D,D-carboxypeptidase | protein | 187 | 41% helix, 16% strand | Q9JN36 |
| B | D,D-DIPEPTIDASE/D,D-carboxypeptidase | protein | 188 | 41% helix, 13% strand | Q9JN36 |
Ligands and binding sites
- DAL · D-alanine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- SO4 · Sulfate ion · ion · chains B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.99 | 20 | empty |
| 2 | 58 | 0.71 | 0.98 | 22 | ZN, DAL |
| 3 | 347 | 0.60 | 0.77 | 57 | empty |
| 4 | 118 | 0.42 | 0.76 | 19 | empty |
| 5 | 102 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4MUT · 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 4MUT · PDBe 4MUT · UniProt Q9JN36
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