Research workbench
Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP.
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
- 2X60
- Type
- protein
- Length
- 666 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
- GTP, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) | protein | 333 | 38% helix, 26% strand | Q9X0C3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 780 | 0.77 | 0.81 | 64 | GTP, MG |
| 2 | 689 | 0.77 | 0.82 | 58 | GTP, MG |
| 3 | 52 | 0.40 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1385 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2X60 · Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP. · 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 2X60 · PDBe 2X60 · UniProt Q9X0C3
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