Research workbench
Crystal structure of mannosyl-3-phosphoglycerate synthase from pyrococcus horikoshii
Analyse Crystal structure of mannosyl-3-phosphoglycerate synthase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZU9
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-3-phosphoglycerate synthase
- EC
- 2.4.1.217
- UniProt
- O58689
- Ligands
- GDP, CO
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 369 | 44% helix, 18% strand | O58689 |
| B | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 359 | 43% helix, 18% strand | O58689 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.69 | 0.82 | 42 | GDP |
| 2 | 518 | 0.69 | 0.79 | 50 | GDP, CO |
| 3 | 55 | 0.41 | 0.81 | 10 | empty |
| 4 | 126 | 0.40 | 0.74 | 19 | empty |
| 5 | 85 | 0.38 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1263 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2ZU9 · Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O58689 · AlphaFold monomer V2.0 prediction for mannosyl-3-phosphoglycerate synthase (O58689) · a predicted model of the same protein · chain B 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 O58689
- Elsewhere: RCSB PDB 2ZU9 · PDBe 2ZU9 · UniProt O58689
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