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Crystal structure of human GDP-D-mannose 4,6-dehydratase

Analyse Crystal structure of human GDP-D-mannose 4,6-dehydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T2A
Type: protein
Length: 1,351 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-mannose 4,6 dehydratase
EC: 4.2.1.47
UniProt: O60547
Ligands: NDP, GDP
Pockets: 13 · best druggability 0.91

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	GDP-mannose 4,6 dehydratase (EC 4.2.1.47)	protein	338	43% helix, 19% strand	O60547
D	GDP-mannose 4,6 dehydratase (EC 4.2.1.47)	protein	337	42% helix, 19% strand	O60547

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C
GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

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	1057	0.91	0.94	138	NDP, GDP
2	1045	0.91	0.94	140	NDP, GDP
3	185	0.81	0.96	30	empty
4	189	0.62	0.83	33	empty
5	150	0.58	0.83	31	empty

Interfaces

6 interfaces between chains.

B–C · 1276 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1271 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1252 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1245 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 319 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1T2A · Crystal structure of human GDP-D-mannose 4,6-dehydratase · the same entry in another collection · chain A against A, TM-score 1.00
O60547 · AlphaFold monomer V2.0 prediction for GDP-mannose 4,6 dehydratase (O60547) · a predicted model of the same protein · chain D 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 O60547
Elsewhere: RCSB PDB 1T2A · PDBe 1T2A · UniProt O60547

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