Research workbench
Crystal structure of oxidized udp-galactopyranose mutase
Analyse Crystal structure of oxidized udp-galactopyranose mutase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DSG
- Type
- protein
- Length
- 939 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactopyranose mutase
- EC
- 5.4.99.9
- UniProt
- Q4E1W2
- Ligands
- FAD, UDP, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 473 | 38% helix, 22% strand | Q4E1W2 |
| B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 466 | 38% helix, 22% strand | Q4E1W2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.86 | 0.87 | 92 | FAD, UDP |
| 2 | 843 | 0.86 | 0.88 | 87 | FAD, UDP |
| 3 | 136 | 0.76 | 0.94 | 28 | empty |
| 4 | 1013 | 0.72 | 0.75 | 81 | empty |
| 5 | 113 | 0.44 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4DSG · Crystal Structure of oxidized UDP-Galactopyranose mutase · 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 Q4E1W2
- Elsewhere: RCSB PDB 4DSG · PDBe 4DSG · UniProt Q4E1W2
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