Research workbench
Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3- epimerase from campylobacter jejuni, serotype HS:3
Analyse Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3- epimerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DAK
- Type
- protein
- Length
- 353 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase
- EC
- 5.-.-.-
- UniProt
- F2X702
- Ligands
- GDP, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase (EC 5.-.-.-) | protein | 178 | 8% helix, 48% strand | F2X702 |
| B | GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase (EC 5.-.-.-) | protein | 175 | 9% helix, 49% strand | F2X702 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- TMA · Tetramethylammonium ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.73 | 0.88 | 35 | GDP, CL |
| 2 | 259 | 0.66 | 0.83 | 33 | GDP, CL |
| 3 | 67 | 0.30 | 0.74 | 13 | empty |
| 4 | 67 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1773 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 8DAK · Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from… · the same entry in another collection · chain B against B, 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 F2X702
- Elsewhere: RCSB PDB 8DAK · PDBe 8DAK · UniProt F2X702
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