MolNFT v1 · #73810 · protein + DNA
Human parp-1 zinc finger 2 (ZN2) bound to DNA
3ODC · Poly [ADP-ribose] polymerase 1: “Human parp-1 zinc finger 2 (ZN2) bound to DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.78). MolNFT v1 #73810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ODC
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1; 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'…
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 93 | 29% helix, 31% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 100 | 25% helix, 20% strand | P09874 |
| C, E | 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3' | dna | 8 | — | — |
| D, F | 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3' | dna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.78 | 0.87 | 48 | empty |
| 2 | 366 | 0.59 | 0.77 | 35 | empty |
| 3 | 72 | 0.40 | 0.79 | 17 | empty |
| 4 | 67 | 0.29 | 0.74 | 8 | empty |
| 5 | 53 | 0.24 | 0.73 | 9 | empty |
Interfaces
9 interfaces between chains.
- A–B · 701 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 380 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–D · 375 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- B–E · 368 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3ODC · Human PARP-1 zinc finger 2 (Zn2) bound to 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 3ODC · PDBe 3ODC · UniProt P09874
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