MolNFT v1 · #159331 · protein
Caenorhabditis elegans udp-glucose dehydrogenase in complex with udp- xylose
6OM8 · Udp-glucose 6-dehydrogenase: “Caenorhabditis elegans udp-glucose dehydrogenase in complex with udp- xylose”. X-ray diffraction, 1 ligand (UDX), 20 pockets (best druggability 0.83). MolNFT v1 #159331 on GenesisL1: 3D structure…
- PDB
- 6OM8
- Type
- protein
- Length
- 5,552 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 6-dehydrogenase
- EC
- 1.1.1.22
- UniProt
- Q19905
- Ligands
- UDX
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 463 | 47% helix, 14% strand | Q19905 |
| D | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 468 | 46% helix, 14% strand | Q19905 |
| E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 461 | 47% helix, 14% strand | Q19905 |
| F | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 465 | 47% helix, 14% strand | Q19905 |
| G, H, I | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 462 | 47% helix, 14% strand | Q19905 |
| J | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 456 | 47% helix, 14% strand | Q19905 |
| K | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 464 | 47% helix, 14% strand | Q19905 |
| L | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 463 | 47% helix, 14% strand | Q19905 |
Ligands and binding sites
- UDX · Uridine-5'-diphosphate-xylopyranose · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.83 | 0.86 | 105 | UDX |
| 2 | 968 | 0.81 | 0.83 | 121 | UDX |
| 3 | 1088 | 0.80 | 0.82 | 116 | UDX |
| 4 | 1025 | 0.79 | 0.81 | 103 | UDX |
| 5 | 925 | 0.79 | 0.81 | 102 | UDX |
Interfaces
21 interfaces between chains.
- I–J · 2674 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2650 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2649 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2637 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2637 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6OM8 · Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose · the same entry in another collection · chain L against L, 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 Q19905
- Elsewhere: RCSB PDB 6OM8 · PDBe 6OM8 · UniProt Q19905
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