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Crystal structure of nicotinate dehydrogenase

Analyse Crystal structure of nicotinate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HRD
Type: protein
Length: 2,400 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinate dehydrogenase large molybdopterin subunit; Nicotinate dehydrogenase medium…
UniProt: Q0QLF2, Q0QLF1, Q0QLF4, Q0QLF3
Ligands: FES, MOS, MCN, NIO, FAD, MG, CA, NO3, SE
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Nicotinate dehydrogenase large molybdopterin subunit	protein	420	29% helix, 27% strand	Q0QLF2
B, F	Nicotinate dehydrogenase medium molybdopterin subunit	protein	330	30% helix, 24% strand	Q0QLF1
C	Nicotinate dehydrogenase FAD-subunit	protein	291	38% helix, 24% strand	Q0QLF4
D	Nicotinate dehydrogenase small fes subunit	protein	160	39% helix, 19% strand	Q0QLF3
G	Nicotinate dehydrogenase FAD-subunit	protein	292	36% helix, 23% strand	Q0QLF4
H	Nicotinate dehydrogenase small fes subunit	protein	157	39% helix, 19% strand	Q0QLF3

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, D, E, H
MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains A, B, E, F
MCN · Pterin cytosine dinucleotide · ligand · 2 copies · chains A, B, D, E, F, H
NIO · Nicotinic acid · ligand · 2 copies · chains A, B, E, F
FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains C, D, G, H
MG · Magnesium ion · metal · 2 copies · chains A
CA · Calcium ion · metal · chains E
NO3 · Nitrate ion · ion · 3 copies · chains A, C, E
SE · Selenium atom · ion · 2 copies · chains A, B, E, F

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.85	0.97	39	SE, MOS, MCN
2	1005	0.84	0.85	102	NIO
3	231	0.84	0.96	41	SE, MOS, MCN
4	577	0.82	0.87	61	FAD
5	517	0.81	0.88	62	FAD

Interfaces

18 interfaces between chains.

E–F · 4799 Å² buried · 83 hydrogen bonds · protein-protein
A–B · 4710 Å² buried · 82 hydrogen bonds · protein-protein
C–D · 1264 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1239 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1132 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3HRD · Crystal structure of nicotinate dehydrogenase · the same entry in another collection · chain H against H, TM-score 1.00
Q0QLF2 · AlphaFold monomer V2.0 prediction for nicotinate dehydrogenase large molybdopterin… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q0QLF3 · AlphaFold monomer V2.0 prediction for nicotinate dehydrogenase small fes subunit (Q0QLF3) · a predicted model of the same protein · chain H against A, TM-score 0.98
Q0QLF1 · AlphaFold monomer V2.0 prediction for nicotinate dehydrogenase medium molybdopterin… · a predicted model of the same protein · chain B against A, TM-score 0.98
Q0QLF4 · AlphaFold monomer V2.0 prediction for nicotinate dehydrogenase FAD- subunit (Q0QLF4) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q0QLF2
Every structure of UniProt Q0QLF1
Every structure of UniProt Q0QLF4
Every structure of UniProt Q0QLF3
Elsewhere: RCSB PDB 3HRD · PDBe 3HRD · UniProt Q0QLF2 · UniProt Q0QLF1 · UniProt Q0QLF4 · UniProt Q0QLF3

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