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Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with mannose-1-phosphate.
Analyse Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X65
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-1-phosphate guanylyltransferase
- EC
- 2.7.7.13
- UniProt
- Q9X0C3
- Ligands
- M1P, MG, PO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) | protein | 334 | 37% helix, 28% strand | Q9X0C3 |
Ligands and binding sites
- M1P · 1-O-phosphono-alpha-D-mannopyranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.73 | 0.79 | 66 | M1P, MG |
| 2 | 579 | 0.72 | 0.80 | 66 | M1P, MG |
| 3 | 84 | 0.33 | 0.74 | 17 | empty |
| 4 | 62 | 0.31 | 0.75 | 13 | empty |
| 5 | 64 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1410 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2X65 · Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with… · 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 Q9X0C3
- Elsewhere: RCSB PDB 2X65 · PDBe 2X65 · UniProt Q9X0C3
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