MolNFT v1 · #92606 · protein
Crystal structure of NADPH-reduced aspergillus fumigatus udp- galactopyranose
4GDE · Udp-galactopyranose mutase: “Crystal structure of NADPH-reduced aspergillus fumigatus udp- galactopyranose”. X-ray diffraction, 2 ligands (FDA, SO4), 17 pockets (best druggability 0.79). MolNFT v1 #92606 on GenesisL1: 3D structure…
- PDB
- 4GDE
- Type
- protein
- Length
- 2,017 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactopyranose mutase
- EC
- 5.4.99.9
- UniProt
- Q4W1X2
- Ligands
- FDA, SO4
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 504 | 38% helix, 24% strand | Q4W1X2 |
| C | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 505 | 38% helix, 24% strand | Q4W1X2 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.79 | 0.80 | 95 | FDA |
| 2 | 1194 | 0.79 | 0.80 | 90 | FDA |
| 3 | 1194 | 0.78 | 0.80 | 99 | FDA |
| 4 | 1179 | 0.78 | 0.80 | 94 | FDA |
| 5 | 72 | 0.74 | 0.98 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1201 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1156 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 904 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 896 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GDE · Crystal structure of NADPH-reduced Aspergillus fumigatus UDP-galactopyranose · 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 Q4W1X2
- Elsewhere: RCSB PDB 4GDE · PDBe 4GDE · UniProt Q4W1X2
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