MolNFT v1 · #144786 · protein
Full length hugdh with A104L substitution in the absence of ligand
6C4K · Udp-glucose 6-dehydrogenase: “Full length hugdh with A104L substitution in the absence of ligand”. X-ray diffraction, 2 ligands (NA, PO4), 10 pockets (best druggability 0.76). MolNFT v1 #144786 on GenesisL1: 3D structure, binding…
- PDB
- 6C4K
- Type
- protein
- Length
- 1,377 residues
- Chains
- 3
- 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
- NA, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 45% helix, 14% strand | O60701 |
| B | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 462 | 43% helix, 15% strand | O60701 |
| C | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 456 | 43% helix, 14% strand | O60701 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.76 | 0.79 | 91 | PO4 |
| 2 | 848 | 0.75 | 0.79 | 84 | PO4 |
| 3 | 818 | 0.73 | 0.77 | 82 | PO4 |
| 4 | 86 | 0.68 | 0.93 | 21 | empty |
| 5 | 178 | 0.61 | 0.83 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 705 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 690 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 681 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6C4K · Full length hUGDH with A104L substitution in the absence of ligand · 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 6C4K · PDBe 6C4K · UniProt O60701
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