Research workbench
Se-met derivatized ugdg, udp-glucose dehydrogenase from sphingomonas elodea
Analyse Se-met derivatized ugdg, udp-glucose dehydrogenase from sphingomonas elodea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A7P
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose dehydrogenase
- EC
- 1.1.1.22
- UniProt
- A4UTT2
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 429 | 43% helix, 13% strand | A4UTT2 |
| B | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 429 | 43% helix, 13% strand | A4UTT2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.79 | 0.81 | 95 | empty |
| 2 | 949 | 0.77 | 0.79 | 87 | NAD |
| 3 | 548 | 0.76 | 0.83 | 66 | NAD |
| 4 | 213 | 0.58 | 0.80 | 28 | empty |
| 5 | 377 | 0.56 | 0.74 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4A7P · Se-Met derivatized UgdG, UDP-glucose dehydrogenase from Sphingomonas elodea · 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 A4UTT2
- Elsewhere: RCSB PDB 4A7P · PDBe 4A7P · UniProt A4UTT2
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