MolNFT v1 · #172591 · protein
Bacillithiol disulfide reductase bdr (ypda) from staphylococcus aureus
7A7B · Ypda family putative bacillithiol disulfide reductase bdr: “Bacillithiol disulfide reductase bdr (ypda) from staphylococcus aureus”. X-ray diffraction, 2 ligands (FAD, NAP), 20 pockets (best druggability 0.84). MolNFT v1 #172591 on…
- PDB
- 7A7B
- Type
- protein
- Length
- 2,526 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ypda family putative bacillithiol disulfide reductase bdr
- UniProt
- A0A0H2WWS2
- Ligands
- FAD, NAP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Ypda family putative bacillithiol disulfide reductase bdr | protein | 323 | 25% helix, 28% strand | A0A0H2WWS2 |
| G | Ypda family putative bacillithiol disulfide reductase bdr | protein | 265 | 20% helix, 24% strand | A0A0H2WWS2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains C, D, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.84 | 0.89 | 63 | FAD, NAP |
| 2 | 493 | 0.84 | 0.90 | 72 | FAD |
| 3 | 757 | 0.83 | 0.86 | 77 | FAD |
| 4 | 523 | 0.83 | 0.89 | 80 | FAD |
| 5 | 460 | 0.83 | 0.90 | 65 | FAD, NAP |
Interfaces
13 interfaces between chains.
- G–H · 1376 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1195 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1185 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1140 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 1022 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7A7B · Bacillithiol Disulfide Reductase Bdr (YpdA) from Staphylococcus aureus · 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 A0A0H2WWS2
- Elsewhere: RCSB PDB 7A7B · PDBe 7A7B · UniProt A0A0H2WWS2
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