MolNFT v1 · #112646 · protein
Crystal structure of udp-glucose 4-epimerase (TM0509) with udp-glucose from hyperthermophilic eubacterium thermotoga maritima
4ZRN: “Crystal structure of udp-glucose 4-epimerase (TM0509) with udp-glucose from hyperthermophilic eubacterium…”. X-ray diffraction, 2 ligands (NAD, UPG), 5 pockets (best druggability 0.83). MolNFT v1 #112646 on GenesisL1: 3D structure…
- PDB
- 4ZRN
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- Q9WYX9
- Ligands
- NAD, UPG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 309 | 41% helix, 18% strand | Q9WYX9 |
| B | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 308 | 42% helix, 18% strand | Q9WYX9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UPG · Uridine-5'-diphosphate-glucose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.83 | 0.84 | 90 | NAD, UPG |
| 2 | 1060 | 0.82 | 0.83 | 84 | NAD, UPG |
| 3 | 239 | 0.53 | 0.76 | 27 | empty |
| 4 | 225 | 0.52 | 0.77 | 25 | empty |
| 5 | 78 | 0.37 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4ZRN · Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) with UDP-glucose from… · 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 Q9WYX9
- Elsewhere: RCSB PDB 4ZRN · PDBe 4ZRN · UniProt Q9WYX9
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