Research workbench
Human POLY(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor abt-888
Analyse Human POLY(ADP-ribose) polymerase 2, catalytic fragment in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KJD
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- 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
- 78P
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 350 | 39% helix, 23% strand | Q9UGN5 |
| B | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) | protein | 352 | 40% helix, 23% strand | Q9UGN5 |
Ligands and binding sites
- 78P · (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.82 | 0.89 | 44 | 78P |
| 2 | 389 | 0.81 | 0.89 | 42 | 78P |
| 3 | 145 | 0.59 | 0.84 | 25 | empty |
| 4 | 109 | 0.57 | 0.85 | 26 | empty |
| 5 | 109 | 0.49 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 312 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3KJD · Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor… · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.97
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 3KJD · PDBe 3KJD · UniProt Q9UGN5
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