MolNFT v1 · #73806 · protein + DNA
Human parp-1 zinc finger 1 (ZN1) bound to DNA
3OD8 · Poly [ADP-ribose] polymerase 1: “Human parp-1 zinc finger 1 (ZN1) bound to DNA”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.52). MolNFT v1 #73806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OD8
- Type
- protein + DNA
- Length
- 782 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1; 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'…
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.52
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, G | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 87 | 29% helix, 28% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 89 | 28% helix, 27% strand | P09874 |
| F | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 90 | 31% helix, 27% strand | P09874 |
| H | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 88 | 27% helix, 27% strand | P09874 |
| I, K, M, O | 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3' | dna | 10 | — | — |
| J, L, N, P | 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.52 | 0.74 | 28 | empty |
| 2 | 154 | 0.39 | 0.73 | 17 | empty |
| 3 | 104 | 0.39 | 0.77 | 15 | empty |
| 4 | 85 | 0.39 | 0.78 | 19 | empty |
| 5 | 102 | 0.38 | 0.76 | 16 | empty |
Interfaces
26 interfaces between chains.
- K–L · 467 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- M–N · 465 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- O–P · 463 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- I–J · 461 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–I · 391 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3OD8 · Human PARP-1 zinc finger 1 (Zn1) bound to DNA · the same entry in another collection · chain L against L, 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 3OD8 · PDBe 3OD8 · UniProt P09874
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