MolNFT v1 · #109177 · protein
Crystal structure of a putative D-mannonate oxidoreductase from haemophilus influenza (AVI_5165, target efi-513796) with bound NAD
4WUV · 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase: “Crystal structure of a putative D-mannonate oxidoreductase from haemophilus influenza (AVI_5165, target…”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.73).…
- PDB
- 4WUV
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase
- UniProt
- C9MHP6
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase | protein | 280 | 46% helix, 14% strand | C9MHP6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.73 | 0.79 | 61 | NAD, EDO |
| 2 | 680 | 0.71 | 0.78 | 60 | NAD, EDO |
| 3 | 180 | 0.47 | 0.75 | 23 | empty |
| 4 | 96 | 0.41 | 0.77 | 16 | empty |
| 5 | 90 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1568 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4WUV · Crystal Structure of a putative D-Mannonate oxidoreductase from Haemophilus influenza… · 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 C9MHP6
- Elsewhere: RCSB PDB 4WUV · PDBe 4WUV · UniProt C9MHP6
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