MolNFT v1 · #76204 · protein

Crystal structure of rdxa from helicobacter pyroli

3QDL · Oxygen-insensitive NADPH nitroreductase: “Crystal structure of rdxa from helicobacter pyroli”. X-ray diffraction, 1 ligand (FMN), 4 pockets (best druggability 0.82). MolNFT v1 #76204 on GenesisL1: 3D structure, binding sites and…

PDB: 3QDL
Type: protein
Length: 686 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxygen-insensitive NADPH nitroreductase
UniProt: O25608
Ligands: FMN
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Oxygen-insensitive NADPH nitroreductase	protein	178	47% helix, 19% strand	O25608
B, D	Oxygen-insensitive NADPH nitroreductase	protein	165	43% helix, 19% strand	O25608

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.82	0.85	108	FMN
2	676	0.78	0.83	84	FMN
3	215	0.56	0.79	35	FMN
4	92	0.40	0.77	13	empty

Interfaces

6 interfaces between chains.

C–D · 3291 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3277 Å² buried · 57 hydrogen bonds · protein-protein
A–C · 617 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 488 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 421 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3QDL · Crystal structure of RdxA from Helicobacter pyroli · the same entry in another collection · chain A against A, TM-score 1.00
O25608 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NADPH nitroreductase (O25608) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O25608
Elsewhere: RCSB PDB 3QDL · PDBe 3QDL · UniProt O25608

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