Research workbench
Human POLY(ADP-ribose) polymerase 12, catalytic fragment in complex with an inhibitor 3-aminobenzoic acid
Analyse Human POLY(ADP-ribose) polymerase 12, 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
- 2PQF
- Type
- protein
- Length
- 1,101 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 12
- EC
- 2.4.2.30
- UniProt
- Q9H0J9
- Ligands
- GAB
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) | protein | 185 | 24% helix, 30% strand | Q9H0J9 |
| B | Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) | protein | 181 | 26% helix, 31% strand | Q9H0J9 |
| C, E | Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) | protein | 185 | 26% helix, 30% strand | Q9H0J9 |
| D | Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) | protein | 182 | 26% helix, 31% strand | Q9H0J9 |
| F | Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) | protein | 183 | 26% helix, 32% strand | Q9H0J9 |
Ligands and binding sites
- GAB · 3-aminobenzoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.78 | 0.84 | 61 | empty |
| 2 | 491 | 0.76 | 0.84 | 39 | empty |
| 3 | 1143 | 0.71 | 0.75 | 102 | empty |
| 4 | 339 | 0.68 | 0.82 | 32 | GAB, CIT |
| 5 | 331 | 0.68 | 0.82 | 32 | GAB, CIT |
Interfaces
9 interfaces between chains.
- D–E · 437 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 396 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 360 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 352 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2PQF · Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment in complex with an inhibitor… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H0J9 · AlphaFold monomer V2.0 prediction for protein mono-ADP- ribosyltransferase PARP12 (Q9H0J9) · a predicted model of the same protein · chain F 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 Q9H0J9
- Elsewhere: RCSB PDB 2PQF · PDBe 2PQF · UniProt Q9H0J9
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