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Crystal structure of oxidized udp-galactopyranose mutase from corynebacterium diphtheriae with udp bound in closed form
Analyse Crystal structure of oxidized udp-galactopyranose mutase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQF
- Type
- protein
- Length
- 771 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
- Q6NER4
- Ligands
- UDP, FAD, 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 | 386 | 39% helix, 19% strand | Q6NER4 |
| B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 385 | 38% helix, 18% strand | Q6NER4 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 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 | 790 | 0.87 | 0.90 | 84 | UDP, FAD |
| 2 | 829 | 0.86 | 0.89 | 89 | UDP, FAD |
| 3 | 403 | 0.66 | 0.80 | 41 | SO4 |
| 4 | 478 | 0.65 | 0.78 | 49 | SO4 |
| 5 | 73 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5EQF · Crystal structure of oxidized UDP-galactopyranose mutase from Corynebacterium diphtheriae… · 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 Q6NER4
- Elsewhere: RCSB PDB 5EQF · PDBe 5EQF · UniProt Q6NER4
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