Research workbench
The complex structure of TIMELESS_PAB and parp-1_CATALYTIC domain
Analyse The complex structure of TIMELESS_PAB and parp-1_CATALYTIC domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XHU
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1; Protein timeless homolog
- EC
- 2.4.2.30
- UniProt
- P09874, Q9UNS1
- Ligands
- CA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 333 | 41% helix, 25% strand | P09874 |
| D | Protein timeless homolog | protein | 83 | 57% helix, 6% strand | Q9UNS1 |
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 341 | 39% helix, 25% strand | P09874 |
| B | Protein timeless homolog | protein | 89 | 51% helix, 6% strand | Q9UNS1 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains C, D, A
- ACT · Acetate ion · additive · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.79 | 0.81 | 118 | GOL, ACT |
| 2 | 457 | 0.78 | 0.86 | 45 | GOL, ACT, CA |
| 3 | 486 | 0.64 | 0.77 | 53 | empty |
| 4 | 195 | 0.62 | 0.83 | 24 | empty |
| 5 | 243 | 0.60 | 0.80 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 804 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 765 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 247 Ų buried · 1 hydrogen bond · protein-protein
- D–A · 170 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 163 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4XHU · The complex structure of Timeless_PAB and PARP-1_catalytic domain · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UNS1 · AlphaFold monomer V2.0 prediction for protein timeless homolog (Q9UNS1) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P09874
- Every structure of UniProt Q9UNS1
- Elsewhere: RCSB PDB 4XHU · PDBe 4XHU · UniProt P09874 · UniProt Q9UNS1
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