Research workbench
Asfv dutpase in complex with dump
Analyse Asfv dutpase in complex with dump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LIS
- Type
- protein
- Length
- 859 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E165R
- UniProt
- A0A2X0SE53
- Ligands
- UMP
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | E165R | protein | 142 | 6% helix, 45% strand | A0A2X0SE53 |
| B, D | E165R | protein | 145 | 8% helix, 43% strand | A0A2X0SE53 |
| C | E165R | protein | 141 | 9% helix, 47% strand | A0A2X0SE53 |
| F | E165R | protein | 144 | 10% helix, 43% strand | A0A2X0SE53 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.72 | 0.82 | 66 | UMP |
| 2 | 280 | 0.68 | 0.83 | 43 | empty |
| 3 | 296 | 0.65 | 0.81 | 43 | empty |
| 4 | 136 | 0.56 | 0.82 | 20 | UMP |
| 5 | 252 | 0.56 | 0.77 | 37 | UMP |
Interfaces
9 interfaces between chains.
- E–F · 846 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 839 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 809 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 768 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LIS · ASFV dUTPase in complex with dUMP · 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 A0A2X0SE53
- Elsewhere: RCSB PDB 6LIS · PDBe 6LIS · UniProt A0A2X0SE53
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