Research workbench
Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3- epimerase from campylobacter jejuni, serotype HS:23/36
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
- 8DCL
- Type
- protein
- Length
- 361 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
- 5.1.3.13
- UniProt
- Q6EF58
- Ligands
- GDP, K, NA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase (EC 5.1.3.13) | protein | 185 | 10% helix, 45% strand | Q6EF58 |
| B | GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase (EC 5.1.3.13) | protein | 176 | 9% helix, 47% strand | Q6EF58 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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 | 230 | 0.66 | 0.84 | 33 | GDP |
| 2 | 219 | 0.64 | 0.83 | 32 | GDP |
| 3 | 67 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1603 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 8DCL · Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase from… · 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 Q6EF58
- Elsewhere: RCSB PDB 8DCL · PDBe 8DCL · UniProt Q6EF58
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