Research workbench
Crystal structure of the human parp-1 DNA binding domain in complex with DNA
Analyse Crystal structure of the human parp-1 DNA binding domain in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AV1
- Type
- protein + DNA
- Length
- 386 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1; 5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3'…
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 86 | 23% helix, 30% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 96 | 25% helix, 25% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 85 | 29% helix, 28% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 95 | 22% helix, 25% strand | P09874 |
| X | 5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3' | dna | 12 | — | — |
| Y | 5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3' | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.42 | 0.76 | 24 | empty |
| 2 | 117 | 0.41 | 0.76 | 19 | empty |
| 3 | 113 | 0.40 | 0.76 | 19 | empty |
| 4 | 83 | 0.31 | 0.74 | 18 | empty |
| 5 | 69 | 0.31 | 0.75 | 12 | empty |
Interfaces
11 interfaces between chains.
- X–Y · 493 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- D–X · 420 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–Y · 412 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–X · 331 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–Y · 316 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4AV1 · Crystal structure of the human PARP-1 DNA binding domain in complex with DNA · 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 P09874
- Elsewhere: RCSB PDB 4AV1 · PDBe 4AV1 · UniProt P09874
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