MolNFT v1 · #121180 · protein
Crystal structure of vancomycin resistance D,D-pentapeptidase vany E175A mutant from vanb-type resistance cassette in complex with ZN(II)
5HNM · D-alanyl-D-alanine carboxypeptidase: “Crystal structure of vancomycin resistance D,D-pentapeptidase vany E175A mutant from vanb-type resistance…”. X-ray diffraction, 2 ligands (ZN, SO4), 19 pockets (best druggability 0.75). MolNFT…
- PDB
- 5HNM
- Type
- protein
- Length
- 1,077 residues
- Chains
- 6
- 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, SO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 179 | 41% helix, 13% strand | Q47746 |
| B | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 181 | 45% helix, 14% strand | Q47746 |
| C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 178 | 44% helix, 13% strand | Q47746 |
| E, F | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 180 | 43% helix, 14% strand | Q47746 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.75 | 0.80 | 85 | ZN, SO4 |
| 2 | 584 | 0.71 | 0.80 | 63 | empty |
| 3 | 174 | 0.64 | 0.85 | 37 | SO4 |
| 4 | 253 | 0.61 | 0.80 | 32 | empty |
| 5 | 132 | 0.54 | 0.82 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–E · 867 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 722 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 296 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 265 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HNM · Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from… · the same entry in another collection · chain F against F, TM-score 1.00
- Q47746 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (Q47746) · a predicted model of the same protein · chain C 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 Q47746
- Elsewhere: RCSB PDB 5HNM · PDBe 5HNM · UniProt Q47746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.