MolNFT v1 · #188325 · protein
Crystal structure of NAD(P)H nitroreductase from klebsiella pneumoniae (short B-axis)
7TMF: “Crystal structure of NAD(P)H nitroreductase from klebsiella pneumoniae (short B-axis)”. X-ray diffraction, 2 ligands (FMN, PO4), 4 pockets (best druggability 0.52). MolNFT v1 #188325 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TMF
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H nitroreductase
- EC
- 1.-.-.-
- UniProt
- A0A237MVZ9
- Ligands
- FMN, PO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 171 | 45% helix, 20% strand | A0A237MVZ9 |
| B | NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 183 | 44% helix, 20% strand | A0A237MVZ9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.52 | 0.79 | 32 | FMN |
| 2 | 109 | 0.51 | 0.81 | 22 | FMN |
| 3 | 102 | 0.46 | 0.79 | 16 | empty |
| 4 | 86 | 0.40 | 0.77 | 17 | PO4 |
Interfaces
1 interface between chains.
- A–B · 2687 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7TMF · Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (short b-axis) · 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 A0A237MVZ9
- Elsewhere: RCSB PDB 7TMF · PDBe 7TMF · UniProt A0A237MVZ9
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