MolNFT v1 · #137707 · protein
Crystal structure of oxidized aspergillus fumigatus udp- galactopyranose mutase complexed with NADH
5VWU · Udp-galactopyranose mutase: “Crystal structure of oxidized aspergillus fumigatus udp- galactopyranose mutase complexed with NADH”. X-ray diffraction, 3 ligands (FAD, NAI, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #137707…
- PDB
- 5VWU
- Type
- protein
- Length
- 1,995 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, NAI, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 494 | 39% helix, 24% strand | Q4W1X2 |
| B | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 494 | 39% helix, 24% strand | Q4W1X2 |
| C | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 503 | 38% helix, 23% strand | Q4W1X2 |
| D | Udp-galactopyranose mutase (EC 5.4.99.9) | protein | 504 | 38% helix, 23% strand | Q4W1X2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- 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
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.82 | 0.83 | 85 | FAD, SO4 |
| 2 | 1091 | 0.81 | 0.82 | 95 | FAD, NAI, SO4 |
| 3 | 1121 | 0.80 | 0.81 | 100 | FAD, NAI, SO4 |
| 4 | 1169 | 0.80 | 0.81 | 104 | FAD, SO4 |
| 5 | 71 | 0.74 | 0.98 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1192 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1169 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 902 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 901 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VWU · 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 5VWU · PDBe 5VWU · UniProt Q4W1X2
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