Research workbench
Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unliganded)
Analyse Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unliganded) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X8J
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-1-phosphate guanylyltransferase 1
- EC
- 2.7.7.13
- UniProt
- O22287
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-1-phosphate guanylyltransferase 1 (EC 2.7.7.13) | protein | 357 | 27% helix, 31% strand | O22287 |
| B | Mannose-1-phosphate guanylyltransferase 1 (EC 2.7.7.13) | protein | 356 | 27% helix, 31% strand | O22287 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 17 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.57 | 0.76 | 37 | SO4 |
| 2 | 172 | 0.48 | 0.76 | 35 | SO4 |
| 3 | 143 | 0.43 | 0.75 | 20 | empty |
| 4 | 114 | 0.42 | 0.76 | 14 | empty |
| 5 | 89 | 0.37 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 624 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7X8J · Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unliganded) · the same entry in another collection · chain A against A, TM-score 1.00
- O22287 · AlphaFold monomer V2.0 prediction for mannose-1-phosphate guanylyltransferase 1 (O22287) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O22287
- Elsewhere: RCSB PDB 7X8J · PDBe 7X8J · UniProt O22287
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