Research workbench
Udp-N-acetylglucosamine 3-dehydrogenase gnna from acidithiobacillus ferrooxidans (P212121)
Analyse Udp-N-acetylglucosamine 3-dehydrogenase gnna from acidithiobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVK
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, NAD-binding
- UniProt
- B7JA34
- Ligands
- NAD, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxidoreductase, NAD-binding | protein | 302 | 39% helix, 29% strand | B7JA34 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 1097 | 0.75 | 0.78 | 93 | SO4 |
| 2 | 481 | 0.60 | 0.74 | 55 | NAD |
| 3 | 84 | 0.36 | 0.76 | 23 | empty |
| 4 | 68 | 0.32 | 0.75 | 16 | empty |
| 5 | 52 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7BVK · UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P212121) · 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 B7JA34
- Elsewhere: RCSB PDB 7BVK · PDBe 7BVK · UniProt B7JA34
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