Research workbench
Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product- bound)
Analyse Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product- bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X8K
- Type
- protein
- Length
- 1,442 residues
- Chains
- 4
- 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
- PPV, GDD, SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-1-phosphate guanylyltransferase 1 (EC 2.7.7.13) | protein | 365 | 27% helix, 30% strand | O22287 |
| B | Mannose-1-phosphate guanylyltransferase 1 (EC 2.7.7.13) | protein | 367 | 27% helix, 30% strand | O22287 |
| C, D | Mannose-1-phosphate guanylyltransferase 1 (EC 2.7.7.13) | protein | 355 | 26% helix, 30% strand | O22287 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains B, D
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · chains A
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.68 | 0.75 | 68 | SO4 |
| 2 | 192 | 0.50 | 0.77 | 31 | GDD |
| 3 | 245 | 0.50 | 0.75 | 42 | PPV |
| 4 | 214 | 0.48 | 0.75 | 36 | empty |
| 5 | 185 | 0.47 | 0.75 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 961 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 717 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7X8K · Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product-bound) · the same entry in another collection · chain D against D, 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 C 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 7X8K · PDBe 7X8K · UniProt O22287
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