Research workbench
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 v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
- Molecule
- Dolichol monophosphate mannose synthase
- UniProt
- Q8U4M3
- Ligands
- GDP, MG, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · resolution 2 · 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.
| Volume (ų) | 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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