MolNFT v1 · #81799 · protein
BD3459, a predatory peptidoglycan endopeptidase from bdellovibrio bacteriovorus
3V39 · D-alanyl-D-alanine carboxypeptidase: “BD3459, a predatory peptidoglycan endopeptidase from bdellovibrio bacteriovorus”. X-ray diffraction, 2 ligands (TAU, SO4), 4 pockets (best druggability 0.47). MolNFT v1 #81799 on GenesisL1: 3D…
- PDB
- 3V39
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- Q6MHT0
- Ligands
- TAU, SO4
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 402 | 33% helix, 22% strand | Q6MHT0 |
Ligands and binding sites
- TAU · 2-aminoethanesulfonic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.47 | 0.79 | 22 | empty |
| 2 | 97 | 0.43 | 0.78 | 22 | PGE |
| 3 | 74 | 0.34 | 0.76 | 23 | TAU |
| 4 | 76 | 0.34 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 3V39 · Bd3459, A Predatory Peptidoglycan Endopeptidase from Bdellovibrio bacteriovorus · 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 Q6MHT0
- Elsewhere: RCSB PDB 3V39 · PDBe 3V39 · UniProt Q6MHT0
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