Research workbench
Crystal structure of rock 1 bound to yb-15-QD37
Analyse Crystal structure of rock 1 bound to yb-15-QD37 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W7P
- Type
- protein
- Length
- 1,545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q13464
- Ligands
- 3J7
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 388 | 41% helix, 15% strand | Q13464 |
| B | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 387 | 40% helix, 15% strand | Q13464 |
| C | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 383 | 41% helix, 15% strand | Q13464 |
| D | Rho-associated protein kinase 1 (EC 2.7.11.1) | protein | 387 | 41% helix, 15% strand | Q13464 |
Ligands and binding sites
- 3J7 · N~1~-[2-(1H-indazol-5-yl)pyrido[3,4-d]pyrimidin-4-yl]-2-methylpropane-1,2-diamine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.74 | 0.79 | 65 | empty |
| 2 | 401 | 0.68 | 0.80 | 42 | 3J7 |
| 3 | 379 | 0.67 | 0.80 | 44 | 3J7 |
| 4 | 381 | 0.67 | 0.80 | 46 | 3J7 |
| 5 | 385 | 0.67 | 0.80 | 40 | 3J7 |
Interfaces
5 interfaces between chains.
- A–B · 2189 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2141 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 175 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4W7P · Crystal Structure of ROCK 1 bound to YB-15-QD37 · 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 Q13464
- Elsewhere: RCSB PDB 4W7P · PDBe 4W7P · UniProt Q13464
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