Research workbench
X-ray structure of the R141 sugar 4,6-dehydratase from acanthamoeba polyphaga minivirus
Analyse X-ray structure of the R141 sugar 4,6-dehydratase from acanthamoeba polyphaga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLO
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dtdp-D-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- Q5UR12
- Ligands
- TYD, NAD, NI
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 319 | 40% helix, 20% strand | Q5UR12 |
| C | Putative dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 312 | 42% helix, 20% strand | Q5UR12 |
| D | Putative dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 307 | 41% helix, 21% strand | Q5UR12 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.85 | 0.89 | 74 | TYD, NAD |
| 2 | 744 | 0.85 | 0.88 | 77 | TYD, NAD |
| 3 | 744 | 0.85 | 0.88 | 76 | TYD, NAD |
| 4 | 775 | 0.84 | 0.87 | 79 | TYD, NAD |
| 5 | 180 | 0.56 | 0.80 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1824 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1687 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 429 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VLO · X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus · 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 Q5UR12
- Elsewhere: RCSB PDB 6VLO · PDBe 6VLO · UniProt Q5UR12
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