MolNFT v1 · #88636 · protein
Crystal structure of dacb from streptococcus pneumoniae D39
4D0Y: “Crystal structure of dacb from streptococcus pneumoniae D39”. X-ray diffraction, 2 ligands (ZN, PO4), 2 pockets (best druggability 0.73). MolNFT v1 #88636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D0Y
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dacb
- EC
- 3.4.17.13
- UniProt
- Q04LP8
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dacb (EC 3.4.17.13) | protein | 184 | 38% helix, 16% strand | Q04LP8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.73 | 0.79 | 82 | PO4 |
| 2 | 52 | 0.47 | 0.86 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 328 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4D0Y · Crystal structure of DacB from Streptococcus pneumoniae D39 · 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 Q04LP8
- Elsewhere: RCSB PDB 4D0Y · PDBe 4D0Y · UniProt Q04LP8
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