MolNFT v1 · #171394 · protein

Low resolution structure of rgnanox

6Z3B · GFO/IDH/MOCA family oxidoreductase: “Low resolution structure of rgnanox”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.83). MolNFT v1 #171394 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Z3B
Type: protein
Length: 737 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GFO/IDH/MOCA family oxidoreductase
UniProt: A0A2N5NNS3
Ligands: NAD
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GFO/IDH/MOCA family oxidoreductase	protein	371	40% helix, 25% strand	A0A2N5NNS3
B	GFO/IDH/MOCA family oxidoreductase	protein	366	40% helix, 26% strand	A0A2N5NNS3

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
CIT · Citric acid · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	693	0.83	0.87	83	NAD, CIT
2	1008	0.82	0.83	113	NAD, CIT
3	79	0.40	0.78	18	empty
4	71	0.38	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 1919 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

6Z3B · Low resolution structure of RgNanOx · 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 A0A2N5NNS3
Elsewhere: RCSB PDB 6Z3B · PDBe 6Z3B · UniProt A0A2N5NNS3

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