Research workbench
GDP-mannose-3', 5' -epimerase (arabidopsis thaliana), with GDP-alpha- D-mannose and GDP-beta-L-galactose bound in the active site.
Analyse GDP-mannose-3', 5' -epimerase (arabidopsis thaliana), with GDP-alpha- D-mannose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C59
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose-3', 5'-epimerase
- EC
- 5.1.3.18
- UniProt
- Q93VR3
- Ligands
- GDD, GDC, NAD
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose-3', 5'-epimerase (EC 5.1.3.18) | protein | 364 | 40% helix, 16% strand | Q93VR3 |
| B | GDP-mannose-3', 5'-epimerase (EC 5.1.3.18) | protein | 362 | 39% helix, 16% strand | Q93VR3 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 2 copies · chains A, B
- GDC · Guanosine-5'-diphosphate-beta-L-galactose · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 8 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.86 | 0.89 | 95 | GDD, GDC, NAD |
| 2 | 656 | 0.85 | 0.89 | 84 | GDD, GDC, NAD |
| 3 | 107 | 0.44 | 0.78 | 16 | empty |
| 4 | 67 | 0.39 | 0.79 | 11 | empty |
| 5 | 58 | 0.37 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2C59 · gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), with gdp-alpha-d-mannose and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q93VR3 · AlphaFold monomer V2.0 prediction for GDP-mannose 3,5-epimerase (Q93VR3) · a predicted model of the same protein · 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 Q93VR3
- Elsewhere: RCSB PDB 2C59 · PDBe 2C59 · UniProt Q93VR3
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