Research workbench
Udp-N-acetylglucosamine 4,6-dehydratase from vibrio fischeri
Analyse Udp-N-acetylglucosamine 4,6-dehydratase from vibrio fischeri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PVZ
- Type
- protein
- Length
- 1,414 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 4,6-dehydratase
- EC
- 4.2.1.-
- UniProt
- Q5E8L1
- Ligands
- NAD, NA, SCN
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-) | protein | 372 | 46% helix, 17% strand | Q5E8L1 |
| B | Udp-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-) | protein | 300 | 46% helix, 13% strand | Q5E8L1 |
| C | Udp-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-) | protein | 371 | 47% helix, 17% strand | Q5E8L1 |
| D | Udp-N-acetylglucosamine 4,6-dehydratase (EC 4.2.1.-) | protein | 371 | 47% helix, 17% strand | Q5E8L1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, D
- SCN · Thiocyanate ion · ion · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.87 | 0.91 | 96 | NAD, SCN |
| 2 | 1200 | 0.85 | 0.86 | 136 | NAD, SCN |
| 3 | 1199 | 0.80 | 0.81 | 116 | empty |
| 4 | 331 | 0.78 | 0.89 | 51 | empty |
| 5 | 1088 | 0.74 | 0.77 | 79 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2436 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2348 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 483 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3PVZ · UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri · 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 Q5E8L1
- Elsewhere: RCSB PDB 3PVZ · PDBe 3PVZ · UniProt Q5E8L1
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