MolNFT v1 · #160286 · protein
Structure of a NAD-dependent persulfide reductase from a. fulgidus
6PFZ · NADH oxidase (noxa-3): “Structure of a NAD-dependent persulfide reductase from a. fulgidus”. X-ray diffraction, 3 ligands (FAD, COA, CA), 18 pockets (best druggability 0.88). MolNFT v1 #160286 on GenesisL1: 3D structure, binding…
- PDB
- 6PFZ
- Type
- protein
- Length
- 2,153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH oxidase (noxa-3)
- UniProt
- O29847
- Ligands
- FAD, COA, CA
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | NADH oxidase (noxa-3) | protein | 536 | 27% helix, 27% strand | O29847 |
| A | NADH oxidase (noxa-3) | protein | 541 | 26% helix, 27% strand | O29847 |
| B | NADH oxidase (noxa-3) | protein | 541 | 26% helix, 26% strand | O29847 |
| C | NADH oxidase (noxa-3) | protein | 535 | 27% helix, 25% strand | O29847 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains D, C, A, B
- COA · Coenzyme A · ligand · 4 copies · chains D, C, A, B
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.88 | 0.89 | 115 | FAD, COA |
| 2 | 990 | 0.88 | 0.89 | 119 | FAD, COA |
| 3 | 1155 | 0.88 | 0.89 | 122 | FAD, COA, CA |
| 4 | 1124 | 0.87 | 0.88 | 123 | FAD, COA |
| 5 | 171 | 0.60 | 0.82 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3978 Ų buried · 51 hydrogen bonds · protein-protein
- D–C · 3774 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PFZ · Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus · the same entry in another collection · chain D against D, 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 O29847
- Elsewhere: RCSB PDB 6PFZ · PDBe 6PFZ · UniProt O29847
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