Research workbench
Human udp-glucose dehydrogenase A225L substitutuion with udp-glucose and NADH bound
Analyse Human udp-glucose dehydrogenase A225L substitutuion with udp-glucose and NADH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C5Z
- Type
- protein
- Length
- 2,612 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
- UPG, NAI
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 454 | 45% helix, 15% strand | O60701 |
| B | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 323 | 46% helix, 11% strand | O60701 |
| C | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 45% helix, 15% strand | O60701 |
| D | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 457 | 45% helix, 16% strand | O60701 |
| E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 45% helix, 15% strand | O60701 |
| F | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 45% helix, 15% strand | O60701 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 6 copies · chains A, B, C, D, E, F
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.80 | 0.82 | 97 | NAI, UPG |
| 2 | 913 | 0.79 | 0.82 | 102 | NAI, UPG |
| 3 | 862 | 0.78 | 0.81 | 85 | NAI, UPG |
| 4 | 836 | 0.77 | 0.81 | 78 | NAI, UPG |
| 5 | 838 | 0.75 | 0.79 | 72 | NAI, UPG |
Interfaces
12 interfaces between chains.
- E–F · 2839 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2819 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2794 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 751 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 728 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6C5Z · Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound · 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 O60701
- Elsewhere: RCSB PDB 6C5Z · PDBe 6C5Z · UniProt O60701
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