MolNFT v1 · #144811 · protein
Human udp-glucose dehydrogenase with udp- glc and NADH bound
6C5A · Udp-glucose 6-dehydrogenase: “Human udp-glucose dehydrogenase with udp- glc and NADH bound”. X-ray diffraction, 2 ligands (NAI, UPG), 17 pockets (best druggability 0.80). MolNFT v1 #144811 on GenesisL1: 3D structure, binding sites…
- PDB
- 6C5A
- Type
- protein
- Length
- 2,751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 6-dehydrogenase
- EC
- 1.1.1.22
- UniProt
- O60701
- Ligands
- NAI, UPG
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 45% helix, 14% strand | O60701 |
| E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 456 | 45% helix, 15% strand | O60701 |
| F | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 46% helix, 15% strand | O60701 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- UPG · Uridine-5'-diphosphate-glucose · ligand · 6 copies · chains A, B, C, D, E, F
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.80 | 0.81 | 112 | NAI, UPG, DMS |
| 2 | 946 | 0.80 | 0.82 | 106 | NAI, UPG, DMS |
| 3 | 937 | 0.79 | 0.81 | 98 | NAI, UPG, DMS |
| 4 | 853 | 0.79 | 0.82 | 90 | NAI, UPG |
| 5 | 850 | 0.79 | 0.82 | 100 | NAI, UPG, DMS |
Interfaces
12 interfaces between chains.
- C–D · 2834 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2825 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2768 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 704 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 692 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6C5A · Human UDP-Glucose Dehydrogenase with UDP- Glc and NADH bound · the same entry in another collection · chain C against C, 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 O60701
- Elsewhere: RCSB PDB 6C5A · PDBe 6C5A · UniProt O60701
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