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Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GlcNAc (open, oxidized)
Analyse Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9D
- Type
- protein
- Length
- 386 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Corynebacterium diphtheriae
- Molecule
- UDP-galactopyranose mutase
- UniProt
- A0A246CDW5
- Ligands
- FAD, UD1, NA
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-galactopyranose mutase | protein | 386 | 40% helix, 19% strand | A0A246CDW5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · chains A
- NA · Sodium ion · metal · chains A
- IPA · Isopropyl alcohol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.81 | 0.82 | 92 | FAD, UD1 |
| 2 | 117 | 0.40 | 0.75 | 20 | empty |
Compared structures
- 6D9D · Crystal structure of corynebacterium diphtheriae udp-galactopyranose mutase 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 A0A246CDW5
- Elsewhere: RCSB PDB 6D9D · PDBe 6D9D · UniProt A0A246CDW5
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