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2.0 a crystal structure of GDP-mannose dehydrogenase

Analyse 2.0 a crystal structure of GDP-mannose dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MUU
Type: protein
Length: 1,744 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-mannose 6-dehydrogenase
EC: 1.1.1.132
UniProt: P11759
Ligands: NAD, GDX, GLC, FRU
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	GDP-mannose 6-dehydrogenase (EC 1.1.1.132)	protein	436	46% helix, 14% strand	P11759

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
GDX · Guanosine 5'-(trihydrogen diphosphate), P'-D-mannopyranosyl ester · ligand · 4 copies · chains A, B, C, D
GLC · alpha-D-glucopyranose · sugar · chains C
FRU · beta-D-fructofuranose · sugar · chains C

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	873	0.82	0.84	85	NAD, GDX
2	828	0.81	0.84	83	NAD, GDX
3	848	0.80	0.83	86	NAD, GDX
4	829	0.80	0.82	83	NAD, GDX
5	535	0.65	0.77	52	empty

Interfaces

6 interfaces between chains.

C–D · 6105 Å² buried · 88 hydrogen bonds · protein-protein
A–B · 5995 Å² buried · 86 hydrogen bonds · protein-protein
A–C · 475 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 431 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 104 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

1MUU · 2.0 A crystal structure of GDP-mannose dehydrogenase · the same entry in another collection · chain D against D, TM-score 1.00
P11759 · AlphaFold monomer V2.0 prediction for GDP-mannose 6-dehydrogenase (P11759) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P11759
Elsewhere: RCSB PDB 1MUU · PDBe 1MUU · UniProt P11759

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