MolNFT v1 · #154348 · protein
Udp-glucose pyrophosphorylase with upg from acinetobacter baumanii
6K8D · UTP--glucose-1-phosphate uridylyltransferase: “Udp-glucose pyrophosphorylase with upg from acinetobacter baumanii”. X-ray diffraction, 2 ligands (UPG, SO4), 15 pockets (best druggability 0.86). MolNFT v1 #154348 on GenesisL1: 3D…
- PDB
- 6K8D
- Type
- protein
- Length
- 1,158 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- X2KZJ9
- Ligands
- UPG, SO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 290 | 32% helix, 20% strand | X2KZJ9 |
| D | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 288 | 35% helix, 22% strand | X2KZJ9 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.86 | 0.88 | 107 | empty |
| 2 | 815 | 0.74 | 0.78 | 72 | UPG, SO4 |
| 3 | 653 | 0.68 | 0.76 | 57 | UPG, SO4 |
| 4 | 192 | 0.67 | 0.86 | 32 | UPG, SO4 |
| 5 | 454 | 0.67 | 0.79 | 61 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2288 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2278 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 812 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 794 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K8D · UDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii · 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 X2KZJ9
- Elsewhere: RCSB PDB 6K8D · PDBe 6K8D · UniProt X2KZJ9
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