Research workbench
Crystal structure of PDE10A2 with fragment ZT0429 (4-methyl-3- nitropyridin-2-amine)
Analyse Crystal structure of PDE10A2 with fragment ZT0429 (4-methyl-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MRZ
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17, 3.1.4.35
- UniProt
- Q9Y233
- Ligands
- 2ZV, NI
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 330 | 71% helix, 0% strand | Q9Y233 |
| B | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 327 | 69% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 2ZV · 4-methyl-3-nitropyridin-2-amine · ligand · chains A
- NI · Nickel (II) ion · metal · 4 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 | 730 | 0.71 | 0.78 | 63 | empty |
| 2 | 317 | 0.71 | 0.84 | 39 | NI |
| 3 | 365 | 0.71 | 0.83 | 38 | 2ZV, NI |
| 4 | 146 | 0.59 | 0.83 | 30 | empty |
| 5 | 83 | 0.47 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4MRZ · Crystal structure of PDE10A2 with fragment ZT0429 (4-methyl-3-nitropyridin-2-amine) · the same entry in another collection · chain A against A, 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 Q9Y233
- Elsewhere: RCSB PDB 4MRZ · PDBe 4MRZ · UniProt Q9Y233
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