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Crystal structure of the wlba (wbpb) dehydrogenase from thermus thermophilus in complex with NAD and udp-glcnaca

Analyse Crystal structure of the wlba (wbpb) dehydrogenase from thermus thermophilus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OA0
Type: protein
Length: 1,237 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccaride biosynthesis protein wbpb
UniProt: Q72KX8
Ligands: NAD, HP7, CL
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Lipopolysaccaride biosynthesis protein wbpb	protein	310	44% helix, 22% strand	Q72KX8
D	Lipopolysaccaride biosynthesis protein wbpb	protein	307	43% helix, 23% strand	Q72KX8

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, D, C
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 · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	352	0.79	0.89	49	NAD, HP7
2	391	0.78	0.87	54	NAD, HP7
3	330	0.77	0.88	50	NAD, HP7
4	320	0.77	0.88	51	NAD, HP7
5	216	0.55	0.78	26	CL

Interfaces

6 interfaces between chains.

C–D · 1030 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1009 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 921 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 881 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3OA0 · Crystal structure of the WlbA (WbpB) Dehydrogenase from Thermus thermophilus in complex… · 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 Q72KX8
Elsewhere: RCSB PDB 3OA0 · PDBe 3OA0 · UniProt Q72KX8

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