MolNFT v1 · #75846 · protein

Crystal structure of the wlba dehydrogenase from bordetella pertussis in complex with NADH and udp-glcnaca

3Q2K · Oxidoreductase: “Crystal structure of the wlba dehydrogenase from bordetella pertussis in complex with NADH and udp-glcnaca”. X-ray diffraction, 2 ligands (NAI, HP7), 20 pockets (best druggability 0.88). MolNFT v1 #75846 on…

PDB: 3Q2K
Type: protein
Length: 5,372 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxidoreductase
UniProt: Q79H45
Ligands: NAI, HP7
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, J, M	Oxidoreductase	protein	346	38% helix, 25% strand	Q79H45
B	Oxidoreductase	protein	329	38% helix, 26% strand	Q79H45
C	Oxidoreductase	protein	347	38% helix, 25% strand	Q79H45
D	Oxidoreductase	protein	343	38% helix, 26% strand	Q79H45
E	Oxidoreductase	protein	321	35% helix, 27% strand	Q79H45
F	Oxidoreductase	protein	327	36% helix, 26% strand	Q79H45
G, H, I, N	Oxidoreductase	protein	342	38% helix, 25% strand	Q79H45
K, P	Oxidoreductase	protein	322	36% helix, 27% strand	Q79H45
L	Oxidoreductase	protein	321	36% helix, 27% strand	Q79H45
O	Oxidoreductase	protein	334	36% helix, 26% strand	Q79H45

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
HP7 · (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid · ligand · 16 copies · chains A, B, C, N, D, E, F, G, H, I, J, K, L, M, O, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	897	0.88	0.91	117	empty
2	1087	0.88	0.90	113	empty
3	1048	0.88	0.89	114	empty
4	1094	0.88	0.89	122	empty
5	1043	0.88	0.89	118	empty

Interfaces

35 interfaces between chains.

A–B · 1888 Å² buried · 18 hydrogen bonds · protein-protein
O–P · 1876 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1873 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1866 Å² buried · 20 hydrogen bonds · protein-protein
K–L · 1864 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3Q2K · Crystal structure of the WlbA dehydrogenase from Bordetella pertussis in complex with… · 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 Q79H45
Elsewhere: RCSB PDB 3Q2K · PDBe 3Q2K · UniProt Q79H45

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