MolNFT v1 · #116930 · protein
Crystal structure of constitutively active parp-2
5DSY · Poly [ADP-ribose] polymerase 2: “Crystal structure of constitutively active parp-2”. X-ray diffraction, 1 ligand (UHB), 15 pockets (best druggability 0.65). MolNFT v1 #116930 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DSY
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 2
- EC
- 2.4.2.30
- UniProt
- Q9UGN5
- Ligands
- UHB
- Pockets
- 15 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 248 | 23% helix, 33% strand | Q9UGN5 |
| B | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 251 | 24% helix, 31% strand | Q9UGN5 |
| D | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 247 | 24% helix, 33% strand | Q9UGN5 |
Ligands and binding sites
- UHB · 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.65 | 0.83 | 25 | empty |
| 2 | 225 | 0.65 | 0.83 | 25 | empty |
| 3 | 274 | 0.62 | 0.80 | 36 | empty |
| 4 | 305 | 0.60 | 0.78 | 26 | UHB |
| 5 | 115 | 0.59 | 0.85 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 5DSY · PDBe 5DSY · UniProt Q9UGN5
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