MolNFT v1 · #191421 · protein

Crystal structure of dihydropteridine REDUCTASE/OXYGEN-insensitive NAD(P)H nitroreductase from klebsiella pneumoniae

8DOR: “Crystal structure of dihydropteridine REDUCTASE/OXYGEN-insensitive NAD(P)H nitroreductase from klebsiella…”. X-ray diffraction, 2 ligands (FMN, PO4), 7 pockets (best druggability 0.71). MolNFT v1 #191421 on GenesisL1: 3D structure…

PDB: 8DOR
Type: protein
Length: 866 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropteridine REDUCTASE/OXYGEN-insensitive NAD(P)H nitroreductase
UniProt: A6T5Y2
Ligands: FMN, PO4
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Dihydropteridine REDUCTASE/OXYGEN-insensitive NAD(P)H nitroreductase	protein	217	56% helix, 15% strand	A6T5Y2
B, D	Dihydropteridine REDUCTASE/OXYGEN-insensitive NAD(P)H nitroreductase	protein	216	55% helix, 15% strand	A6T5Y2

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 10 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	519	0.71	0.80	44	FMN, PO4
2	505	0.71	0.80	50	FMN, PO4, GOL
3	439	0.70	0.81	44	FMN, PO4, GOL
4	364	0.70	0.82	36	FMN, PO4, GOL
5	438	0.63	0.77	51	empty

Interfaces

6 interfaces between chains.

A–B · 3645 Å² buried · 56 hydrogen bonds · protein-protein
C–D · 3590 Å² buried · 56 hydrogen bonds · protein-protein
B–D · 298 Å² buried · 1 hydrogen bond · protein-protein
A–C · 282 Å² buried · 1 hydrogen bond · protein-protein
A–D · 32 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

8DOR · Crystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase… · 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 A6T5Y2
Elsewhere: RCSB PDB 8DOR · PDBe 8DOR · UniProt A6T5Y2

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