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The crystal structure of udp-glucose pyrophosphorylase complexed with udp-glucose
Analyse The crystal structure of udp-glucose pyrophosphorylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JUK
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose pyrophosphorylase (galu)
- EC
- 2.7.7.9
- UniProt
- O25363
- Ligands
- UPG, MG
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose pyrophosphorylase (galu) (EC 2.7.7.9) | protein | 265 | 39% helix, 26% strand | O25363 |
| B | Udp-glucose pyrophosphorylase (galu) (EC 2.7.7.9) | protein | 263 | 40% helix, 26% strand | O25363 |
| C | Udp-glucose pyrophosphorylase (galu) (EC 2.7.7.9) | protein | 264 | 39% helix, 26% strand | O25363 |
| D | Udp-glucose pyrophosphorylase (galu) (EC 2.7.7.9) | protein | 264 | 38% helix, 26% strand | O25363 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.86 | 0.87 | 117 | empty |
| 2 | 442 | 0.76 | 0.85 | 39 | UPG, MG |
| 3 | 431 | 0.76 | 0.85 | 38 | UPG, MG |
| 4 | 426 | 0.74 | 0.84 | 38 | UPG, MG |
| 5 | 434 | 0.73 | 0.83 | 39 | UPG, MG |
Interfaces
6 interfaces between chains.
- C–D · 1733 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 944 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 831 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JUK · The Crystal Structure of UDP-glucose pyrophosphorylase complexed with UDP-glucose · 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 O25363
- Elsewhere: RCSB PDB 3JUK · PDBe 3JUK · UniProt O25363
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