Research workbench
Ligand bound full length hugdh with A104L substitution
Analyse Ligand bound full length hugdh with A104L substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C4J
- Type
- protein
- Length
- 5,483 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
- O60701
- Ligands
- NAD, UPG, CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 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 | 426 | 45% helix, 14% strand | O60701 |
| B, C, D, E, F, G, I, K, L | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 44% helix, 15% strand | O60701 |
| H | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 44% helix, 15% strand | O60701 |
| J | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 458 | 45% helix, 15% strand | O60701 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- UPG · Uridine-5'-diphosphate-glucose · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 13 copies · chains A, B, D, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 8 copies · chains C, D, E, F, B, G, K, L
- PGO · S-1,2-propanediol · additive · 6 copies · chains C, D, E, F, G, H, 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 | 942 | 0.80 | 0.82 | 93 | NAD, UPG |
| 2 | 916 | 0.80 | 0.82 | 96 | NAD, UPG, PGO |
| 3 | 986 | 0.79 | 0.81 | 93 | NAD, UPG |
| 4 | 979 | 0.79 | 0.81 | 96 | NAD, UPG, PGO |
| 5 | 861 | 0.79 | 0.82 | 92 | NAD, UPG |
Interfaces
27 interfaces between chains.
- E–F · 2861 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 2854 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2843 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2841 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 2819 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6C4J · Ligand bound full length hUGDH with A104L substitution · 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 O60701
- Elsewhere: RCSB PDB 6C4J · PDBe 6C4J · UniProt O60701
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