Research workbench
Crystal structure of udp-galactopyranose mutase in complex with udp
Analyse Crystal structure of udp-galactopyranose mutase in complex with udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HE3
- Type
- protein
- Length
- 3,632 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
- UDP, FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 366 | 34% helix, 21% strand | Q9RYF1 |
| B, I | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 364 | 34% helix, 21% strand | Q9RYF1 |
| C, D | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 362 | 35% helix, 22% strand | Q9RYF1 |
| E | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 364 | 33% helix, 22% strand | Q9RYF1 |
| F, G, H | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 363 | 35% helix, 23% strand | Q9RYF1 |
| J | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 361 | 35% helix, 22% strand | Q9RYF1 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- FAD · Flavin-adenine dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
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 | 777 | 0.87 | 0.90 | 77 | UDP, FAD |
| 2 | 673 | 0.87 | 0.91 | 76 | UDP, FAD |
| 3 | 709 | 0.87 | 0.90 | 77 | UDP, FAD |
| 4 | 735 | 0.87 | 0.90 | 82 | UDP, FAD |
| 5 | 716 | 0.86 | 0.90 | 74 | UDP, FAD |
Interfaces
20 interfaces between chains.
- A–I · 1255 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 1219 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 1182 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1181 Ų buried · 15 hydrogen bonds · protein-protein
- D–J · 1175 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3HE3 · Crystal Structure of UDP-galactopyranose mutase in complex with UDP · 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 3HE3 · PDBe 3HE3 · UniProt Q9RYF1
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