Research workbench
Structure of oxidized udp-galactopyranose mutase from mycobacterium smegmatis in complex with udp in opened and closed form
Analyse Structure of oxidized udp-galactopyranose mutase from mycobacterium smegmatis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQD
- Type
- protein
- Length
- 783 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
- A0R629
- Ligands
- FAD, UDP, NO3, SO4
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 392 | 39% helix, 18% strand | A0R629 |
| B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 391 | 39% helix, 19% strand | A0R629 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · chains B
- NO3 · Nitrate ion · ion · 7 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.87 | 0.90 | 92 | UDP, FAD |
| 2 | 1079 | 0.82 | 0.83 | 92 | FAD |
| 3 | 362 | 0.62 | 0.78 | 35 | empty |
| 4 | 314 | 0.60 | 0.78 | 29 | empty |
| 5 | 180 | 0.47 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5EQD · Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex… · 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 A0R629
- Elsewhere: RCSB PDB 5EQD · PDBe 5EQD · UniProt A0R629
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