MolNFT v1 · #47826 · protein
Crystal structure of udp-glucose pyrophosphorylase from corynebacteria glutamicum in complex with magnesium and udp-glucose
2PA4 · UTP-glucose-1-phosphate uridylyltransferase: “Crystal structure of udp-glucose pyrophosphorylase from corynebacteria glutamicum in complex with magnesium…”. X-ray diffraction, 2 ligands (UPG, MG), 13 pockets (best druggability…
- PDB
- 2PA4
- Type
- protein
- Length
- 1,187 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
- Q6M6R3
- Ligands
- UPG, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 294 | 41% helix, 24% strand | Q6M6R3 |
| B, C | UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 299 | 41% helix, 23% strand | Q6M6R3 |
| D | UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 295 | 40% helix, 24% strand | Q6M6R3 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.82 | 0.85 | 106 | empty |
| 2 | 505 | 0.78 | 0.86 | 45 | MG, UPG |
| 3 | 495 | 0.78 | 0.85 | 45 | MG, UPG |
| 4 | 496 | 0.77 | 0.85 | 43 | MG, UPG |
| 5 | 569 | 0.77 | 0.84 | 46 | MG, UPG |
Interfaces
6 interfaces between chains.
- A–D · 2928 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2893 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 214 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 204 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 197 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2PA4 · Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in… · 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 Q6M6R3
- Elsewhere: RCSB PDB 2PA4 · PDBe 2PA4 · UniProt Q6M6R3
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