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Crystal structure of udp-glucose 6-dehydrogenase from porphyromonas gingivalis bound to product udp-glucuronate
Analyse Crystal structure of udp-glucose 6-dehydrogenase from porphyromonas gingivalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GG2
- Type
- protein
- Length
- 1,703 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar dehydrogenase, udp-GLUCOSE/GDP-mannose dehydrogenase family
- EC
- 1.1.1.22
- UniProt
- Q7MVC7
- Ligands
- UGA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar dehydrogenase, udp-GLUCOSE/GDP-mannose dehydrogenase family (EC 1.1.1.22) | protein | 431 | 46% helix, 14% strand | Q7MVC7 |
| B | Sugar dehydrogenase, udp-GLUCOSE/GDP-mannose dehydrogenase family (EC 1.1.1.22) | protein | 425 | 46% helix, 14% strand | Q7MVC7 |
| C | Sugar dehydrogenase, udp-GLUCOSE/GDP-mannose dehydrogenase family (EC 1.1.1.22) | protein | 420 | 46% helix, 14% strand | Q7MVC7 |
| D | Sugar dehydrogenase, udp-GLUCOSE/GDP-mannose dehydrogenase family (EC 1.1.1.22) | protein | 427 | 46% helix, 13% strand | Q7MVC7 |
Ligands and binding sites
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.84 | 0.85 | 107 | UGA |
| 2 | 421 | 0.82 | 0.90 | 58 | UGA |
| 3 | 426 | 0.82 | 0.89 | 58 | UGA |
| 4 | 406 | 0.79 | 0.88 | 53 | UGA |
| 5 | 74 | 0.67 | 0.93 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2850 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2819 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1458 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 958 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3GG2 · Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to… · 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 Q7MVC7
- Elsewhere: RCSB PDB 3GG2 · PDBe 3GG2 · UniProt Q7MVC7
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