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Dolichyl phosphate mannose synthase in complex with GDP and MG2+

Analyse Dolichyl phosphate mannose synthase in complex with GDP and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MLZ
Type: protein
Length: 355 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dolichol monophosphate mannose synthase
UniProt: Q8U4M3
Ligands: GDP, MG, CL
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dolichol monophosphate mannose synthase	protein	355	54% helix, 12% strand	Q8U4M3

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · chains A
LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	543	0.78	0.85	48	GDP, MG
2	191	0.55	0.79	21	CL, LDA
3	77	0.34	0.74	19	empty

Compared structures

5MLZ · Dolichyl phosphate mannose synthase in complex with GDP and Mg2+ · 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 Q8U4M3
Elsewhere: RCSB PDB 5MLZ · PDBe 5MLZ · UniProt Q8U4M3

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