MolNFT v1 · #137706 · protein
Crystal structure of oxidized aspergillus fumigatus udp- galactopyranose mutase complexed with NADPH
5VWT · Udp-galactopyranose mutase: “Crystal structure of oxidized aspergillus fumigatus udp- galactopyranose mutase complexed with NADPH”. X-ray diffraction, 3 ligands (FAD, NDP, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #137706…
- PDB
- 5VWT
- Type
- protein
- Length
- 1,987 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
- FAD, NDP, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 495 | 39% helix, 24% strand | Q4W1X2 |
| B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 492 | 39% helix, 24% strand | Q4W1X2 |
| C | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 501 | 38% helix, 23% strand | Q4W1X2 |
| D | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 499 | 38% helix, 23% strand | Q4W1X2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.81 | 0.82 | 83 | FAD, NDP, SO4 |
| 2 | 1074 | 0.81 | 0.82 | 88 | FAD, NDP, SO4 |
| 3 | 1165 | 0.80 | 0.81 | 89 | FAD, NDP, SO4 |
| 4 | 1147 | 0.80 | 0.81 | 87 | FAD, NDP, SO4 |
| 5 | 97 | 0.60 | 0.87 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1185 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1175 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 902 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 898 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VWT · Crystal structure of oxidized Aspergillus fumigatus UDP-galactopyranose mutase complexed… · 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 5VWT · PDBe 5VWT · UniProt Q4W1X2
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