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Udp-N-acetylglucosamine 3-dehydrogenase gnna from acidithiobacillus ferrooxidans (P21)
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
- 7BVJ
- Type
- protein
- Length
- 1,219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, NAD-binding
- UniProt
- B7JA34
- Ligands
- NAD, F8U
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, NAD-binding | protein | 313 | 41% helix, 28% strand | B7JA34 |
| B | Oxidoreductase, NAD-binding | protein | 302 | 41% helix, 26% strand | B7JA34 |
| C | Oxidoreductase, NAD-binding | protein | 303 | 42% helix, 29% strand | B7JA34 |
| D | Oxidoreductase, NAD-binding | protein | 301 | 42% helix, 27% strand | B7JA34 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- F8U · (2R,3R)-2,3-bis(oxidanyl)butane-1,4-disulfonic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.82 | 0.83 | 107 | F8U |
| 2 | 778 | 0.75 | 0.79 | 69 | empty |
| 3 | 792 | 0.73 | 0.78 | 75 | empty |
| 4 | 741 | 0.70 | 0.76 | 66 | NAD |
| 5 | 567 | 0.64 | 0.75 | 59 | NAD |
Interfaces
5 interfaces between chains.
- A–B · 1263 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 984 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 602 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BVJ · UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21) · the same entry in another collection · chain B against B, 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 7BVJ · PDBe 7BVJ · UniProt B7JA34
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