MolNFT v1 · #135176 · protein
Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from vibrio cholerae O1 biovar eltor str. N16961
5TR7: “Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from vibrio cholerae O1 biovar eltor str.…”. X-ray diffraction, 1 ligand (NO2), 5 pockets (best druggability 0.75). MolNFT v1 #135176 on GenesisL1: 3D structure…
- PDB
- 5TR7
- Type
- protein
- Length
- 751 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- A0A0H7A7Y4
- Ligands
- NO2
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 251 | 41% helix, 24% strand | A0A0H7A7Y4 |
| B | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 249 | 40% helix, 24% strand | A0A0H7A7Y4 |
Ligands and binding sites
- NO2 · Nitrite ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.75 | 0.78 | 87 | empty |
| 2 | 303 | 0.59 | 0.77 | 38 | GOL |
| 3 | 111 | 0.43 | 0.78 | 20 | empty |
| 4 | 89 | 0.38 | 0.76 | 16 | empty |
| 5 | 64 | 0.34 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 636 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5TR7 · Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae… · 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 A0A0H7A7Y4
- Elsewhere: RCSB PDB 5TR7 · PDBe 5TR7 · UniProt A0A0H7A7Y4
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