MolNFT v1 · #93432 · protein

Crystal structure of NDOR1

4H2D · NADPH-dependent diflavin oxidoreductase 1: “Crystal structure of NDOR1”. X-ray diffraction, 1 ligand (FMN), 4 pockets (best druggability 0.47). MolNFT v1 #93432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4H2D
Type: protein
Length: 311 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADPH-dependent diflavin oxidoreductase 1
EC: 1.6.-.-
UniProt: Q9UHB4
Ligands: FMN
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NADPH-dependent diflavin oxidoreductase 1 (EC 1.6.-.-)	protein	158	41% helix, 22% strand	Q9UHB4
B	NADPH-dependent diflavin oxidoreductase 1 (EC 1.6.-.-)	protein	153	40% helix, 22% strand	Q9UHB4

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.47	0.80	28	empty
2	92	0.41	0.78	23	FMN
3	83	0.41	0.78	22	FMN
4	59	0.27	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 742 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4H2D · Crystal structure of NDOR1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHB4 · AlphaFold monomer V2.0 prediction for NADPH-dependent diflavin oxidoreductase 1 (Q9UHB4) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9UHB4
Elsewhere: RCSB PDB 4H2D · PDBe 4H2D · UniProt Q9UHB4

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