MolNFT v1 · #110490 · protein

Granulicella M. formate dehydrogenase (fdh) in complex with NAD(+)

4XYE: “Granulicella M. formate dehydrogenase (fdh) in complex with NAD(+)”. X-ray diffraction, 1 ligand (NAD), 6 pockets (best druggability 0.81). MolNFT v1 #110490 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XYE
Type: protein
Length: 768 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Formate dehydrogenase
EC: 1.2.1.2
UniProt: G8NVB5
Ligands: NAD
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Formate dehydrogenase (EC 1.2.1.2)	protein	384	36% helix, 17% strand	G8NVB5

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.81	0.83	128	NAD
2	264	0.58	0.79	55	empty
3	190	0.58	0.81	28	empty
4	182	0.56	0.80	27	empty
5	125	0.50	0.80	17	empty

Interfaces

1 interface between chains.

A–B · 3755 Å² buried · 52 hydrogen bonds · protein-protein

Compared structures

4XYE · Granulicella M. formate dehydrogenase (fdh) in complex with NAD(+) · 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 G8NVB5
Elsewhere: RCSB PDB 4XYE · PDBe 4XYE · UniProt G8NVB5

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