MolNFT v1 · #167545 · protein
Crystal structure of CJ1427, an essential NAD-dependent dehydrogenase from campylobacter jejuni, in the presence of NADH and GDP
6VO6 · Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE: “Crystal structure of CJ1427, an essential NAD-dependent dehydrogenase from campylobacter jejuni, in the…”. X-ray diffraction, 4 ligands (NAI, GDP, NA), 6 pockets (best druggability…
- PDB
- 6VO6
- Type
- protein
- Length
- 1,225 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE
- EC
- 5.1.3.2
- UniProt
- Q0P8I7
- Ligands
- NAI, GDP, NA, CL
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE (EC 5.1.3.2) | protein | 307 | 39% helix, 19% strand | Q0P8I7 |
| B | Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE (EC 5.1.3.2) | protein | 310 | 38% helix, 19% strand | Q0P8I7 |
| C | Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE (EC 5.1.3.2) | protein | 297 | 39% helix, 20% strand | Q0P8I7 |
| D | Putative sugar-nucleotide EPIMERASE/DEHYDRATEASE (EC 5.1.3.2) | protein | 311 | 38% helix, 20% strand | Q0P8I7 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- TMA · Tetramethylammonium ion · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.88 | 0.94 | 93 | NAI, EDO |
| 2 | 659 | 0.82 | 0.87 | 75 | NAI, GDP, EDO |
| 3 | 516 | 0.82 | 0.88 | 71 | NAI, GDP, EDO |
| 4 | 137 | 0.72 | 0.91 | 40 | empty |
| 5 | 51 | 0.50 | 0.87 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1460 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1407 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1370 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1366 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 810 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VO6 · Crystal Structure of Cj1427, an Essential NAD-dependent Dehydrogenase 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 Q0P8I7
- Elsewhere: RCSB PDB 6VO6 · PDBe 6VO6 · UniProt Q0P8I7
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