MolNFT v1 · #145836 · protein
2.2 ångström resolution crystal structure oxygen-insensitive NAD(P)H- dependent nitroreductase nfsb from vibrio vulnificus in complex with FMN
6CZP · Oxygen-insensitive NAD(P)H nitroreductase: “2.2 ångström resolution crystal structure oxygen-insensitive NAD(P)H- dependent nitroreductase nfsb from…”. X-ray diffraction, 2 ligands (FMN, CL), 20 pockets (best druggability 0.78).…
- PDB
- 6CZP
- Type
- protein
- Length
- 1,746 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- UniProt
- A0A1W6MCC0
- Ligands
- FMN, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Oxygen-insensitive NAD(P)H nitroreductase | protein | 219 | 54% helix, 15% strand | A0A1W6MCC0 |
| B, D, F, H | Oxygen-insensitive NAD(P)H nitroreductase | protein | 218 | 52% helix, 15% strand | A0A1W6MCC0 |
| G | Oxygen-insensitive NAD(P)H nitroreductase | protein | 217 | 53% helix, 15% strand | A0A1W6MCC0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 3 copies · chains C, D, G
- GOL · Glycerol · additive · 3 copies · chains A, B, E, G, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 3 copies · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.78 | 0.83 | 72 | empty |
| 2 | 632 | 0.77 | 0.83 | 68 | empty |
| 3 | 629 | 0.75 | 0.82 | 57 | GOL |
| 4 | 542 | 0.75 | 0.82 | 48 | empty |
| 5 | 378 | 0.74 | 0.85 | 42 | FMN, GOL |
Interfaces
17 interfaces between chains.
- C–D · 3594 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 3566 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 3551 Ų buried · 66 hydrogen bonds · protein-protein
- G–H · 3530 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 573 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6CZP · 2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent… · 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 A0A1W6MCC0
- Elsewhere: RCSB PDB 6CZP · PDBe 6CZP · UniProt A0A1W6MCC0
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