Research workbench
Structure of ARTD2/PARP2 wgr domain bound to double strand DNA with 5 nucleotide overhang and 5'PHOSPHATE
Analyse Structure of ARTD2/PARP2 wgr domain bound to double strand DNA with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F5F
- Type
- protein + DNA
- Length
- 521 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 2; DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)…
- EC
- 2.4.2.30
- UniProt
- Q9UGN5
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 116 | 16% helix, 41% strand | Q9UGN5 |
| C | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 115 | 17% helix, 42% strand | Q9UGN5 |
| D | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 114 | 17% helix, 41% strand | Q9UGN5 |
| E, F, G, H | DNA (5'-D(P*CP*GP*GP*TP*CP*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)- 3') | dna | 15 | — | — |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.54 | 0.75 | 30 | empty |
| 2 | 231 | 0.46 | 0.73 | 20 | empty |
| 3 | 77 | 0.39 | 0.78 | 12 | empty |
| 4 | 98 | 0.39 | 0.76 | 17 | empty |
| 5 | 107 | 0.36 | 0.74 | 17 | empty |
Interfaces
8 interfaces between chains.
- E–F · 448 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- G–H · 445 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- D–G · 321 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–F · 276 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–H · 256 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6F5F · Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UGN5 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 2 (Q9UGN5) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9UGN5
- Elsewhere: RCSB PDB 6F5F · PDBe 6F5F · UniProt Q9UGN5
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