Research workbench
Crystal structure of udp-galactopyranose mutase from corynebacterium diphtheriae in complex with 2-[4-(4-chlorophenyl)-7-(2-thienyl)-2- thia-5,6,8,9-TETRAZABICYCLO[4.3.0]NONA-4,7,9-trien-3-YL]ACETIC
Analyse Crystal structure of 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
- 4XGK
- Type
- protein
- Length
- 772 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
- 40K, FDA, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 386 | 39% helix, 18% strand | Q6NER4 |
Ligands and binding sites
- 40K · [(7S)-6-(4-chlorophenyl)-3-(thiophen-2-yl)-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-7-yl]acetic acid · ligand · 2 copies · chains A, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 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 | 1044 | 0.83 | 0.84 | 94 | 40K, FDA |
| 2 | 1011 | 0.81 | 0.82 | 94 | 40K, FDA |
| 3 | 427 | 0.65 | 0.79 | 45 | empty |
| 4 | 387 | 0.65 | 0.79 | 36 | SO4 |
| 5 | 108 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1017 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4XGK · Crystal structure of UDP-galactopyranose mutase from Corynebacterium diphtheriae in… · 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 4XGK · PDBe 4XGK · UniProt Q6NER4
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