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Crystal structure of udp-glucose 4-epimerase (TM0509) from hyperthermophilic eubacterium thermotoga maritima
Analyse Crystal structure of udp-glucose 4-epimerase (TM0509) from hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZRM
- Type
- protein
- Length
- 616 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
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 308 | 42% 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
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.80 | 0.89 | 49 | NAD, GOL |
| 2 | 355 | 0.78 | 0.88 | 49 | NAD, GOL |
| 3 | 474 | 0.75 | 0.84 | 38 | empty |
| 4 | 384 | 0.74 | 0.84 | 41 | empty |
| 5 | 255 | 0.54 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1355 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4ZRM · Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hyperthermophilic Eubacterium… · 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 4ZRM · PDBe 4ZRM · UniProt Q9WYX9
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