Research workbench
Xpd mechanism
Analyse Xpd mechanism in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H8W
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase TA0057; DNA (5'-D(P*TP*AP*CP*GP*A)-3')
- EC
- 3.6.4.12
- UniProt
- Q9HM14
- Ligands
- SF4, NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase TA0057 (EC 3.6.4.12) | protein | 596 | 54% helix, 14% strand | Q9HM14 |
| E | DNA (5'-D(P*TP*AP*CP*GP*A)-3') | dna | 4 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.73 | 0.78 | 72 | empty |
| 2 | 266 | 0.64 | 0.81 | 30 | empty |
| 3 | 236 | 0.57 | 0.78 | 36 | empty |
| 4 | 176 | 0.51 | 0.78 | 20 | empty |
| 5 | 56 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–E · 733 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
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 Q9HM14
- Elsewhere: RCSB PDB 5H8W · PDBe 5H8W · UniProt Q9HM14
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