Research workbench
Crystal structure of udp-galactopyranose mutase (reduced form) in complex with substrate
Analyse Crystal structure of udp-galactopyranose mutase (reduced form) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HDY
- Type
- protein
- Length
- 3,600 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactopyranose mutase
- EC
- 5.4.99.9
- UniProt
- Q9RYF1
- Ligands
- GDU, FAD, FDA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 365 | 34% helix, 22% strand | Q9RYF1 |
| B, D, E, I | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 361 | 34% helix, 22% strand | Q9RYF1 |
| C | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 349 | 34% helix, 19% strand | Q9RYF1 |
| F | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 362 | 33% helix, 22% strand | Q9RYF1 |
| G | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 360 | 34% helix, 23% strand | Q9RYF1 |
| H | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 361 | 34% helix, 22% strand | Q9RYF1 |
| J | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 359 | 34% helix, 21% strand | Q9RYF1 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- FAD · Flavin-adenine dinucleotide · ligand · 7 copies · chains A, C, E, F, H, I, J
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 3 copies · chains B, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.87 | 0.90 | 82 | GDU, FDA |
| 2 | 695 | 0.87 | 0.91 | 80 | FAD, GDU |
| 3 | 753 | 0.87 | 0.90 | 80 | FAD, GDU |
| 4 | 739 | 0.87 | 0.90 | 76 | FAD, GDU |
| 5 | 724 | 0.87 | 0.90 | 77 | GDU, FDA |
Interfaces
20 interfaces between chains.
- B–H · 1206 Ų buried · 24 hydrogen bonds · protein-protein
- A–I · 1200 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 1184 Ų buried · 20 hydrogen bonds · protein-protein
- D–J · 1153 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1147 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3HDY · Crystal Structure of UDP-galactopyranose mutase (reduced form) in complex with substrate · 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 Q9RYF1
- Elsewhere: RCSB PDB 3HDY · PDBe 3HDY · UniProt Q9RYF1
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