MolNFT v1 · #181649 · protein
Crystal structure of CJ1428, a GDP-D-glycero-L-gluco-heptose synthase from campylobacter jejuni in the presence of NADPH
7M13 · GDP-L-fucose synthase: “Crystal structure of CJ1428, a GDP-D-glycero-L-gluco-heptose synthase from campylobacter jejuni in the…”. X-ray diffraction, 2 ligands (NAP, MG), 3 pockets (best druggability 0.79). MolNFT v1 #181649 on…
- PDB
- 7M13
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-L-fucose synthase
- EC
- 1.1.1.271
- UniProt
- Q0P8I6
- Ligands
- NAP, MG
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 338 | 46% helix, 13% strand | Q0P8I6 |
| B | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 340 | 45% helix, 14% strand | Q0P8I6 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 901 | 0.79 | 0.81 | 77 | NAP |
| 2 | 631 | 0.71 | 0.79 | 65 | NAP |
| 3 | 130 | 0.44 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1832 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7M13 · Crystal structure of CJ1428, a GDP-D-GLYCERO-L-GLUCO-HEPTOSE SYNTHASE from campylobacter… · 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 Q0P8I6
- Elsewhere: RCSB PDB 7M13 · PDBe 7M13 · UniProt Q0P8I6
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