Research workbench
Structure of the shewanella loihica pv-4 NADH-dependent persulfide reductase C43S/C531S double mutant
Analyse Structure of the shewanella loihica pv-4 NADH-dependent persulfide reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NT6
- Type
- protein
- Length
- 1,130 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent pyridine nucleotide-disulphide oxidoreductase
- EC
- 1.8.1.14
- UniProt
- A3QAV3
- Ligands
- FAD, COA, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FAD-dependent pyridine nucleotide-disulphide oxidoreductase (EC 1.8.1.14) | protein | 565 | 29% helix, 27% strand | A3QAV3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.86 | 0.87 | 134 | FAD, COA |
| 2 | 1052 | 0.81 | 0.82 | 127 | FAD |
| 3 | 787 | 0.79 | 0.82 | 58 | COA, CL |
| 4 | 298 | 0.56 | 0.77 | 40 | empty |
| 5 | 52 | 0.42 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3753 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3NT6 · Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C43S/C531S… · 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 A3QAV3
- Elsewhere: RCSB PDB 3NT6 · PDBe 3NT6 · UniProt A3QAV3
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