Research workbench
PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin- 1-yl)-dibenzodiazepine
Analyse PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZJI
- Type
- protein
- Length
- 1,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 1
- EC
- 2.7.11.1
- UniProt
- Q13153
- Ligands
- 4OQ, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 278 | 44% helix, 18% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 276 | 44% helix, 18% strand | Q13153 |
| C | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 281 | 43% helix, 16% strand | Q13153 |
| D | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 280 | 43% helix, 18% strand | Q13153 |
Ligands and binding sites
- 4OQ · 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.80 | 0.89 | 31 | 4OQ |
| 2 | 347 | 0.78 | 0.88 | 34 | 4OQ |
| 3 | 291 | 0.76 | 0.88 | 38 | 4OQ |
| 4 | 973 | 0.76 | 0.79 | 108 | empty |
| 5 | 186 | 0.76 | 0.91 | 23 | 4OQ |
Interfaces
6 interfaces between chains.
- A–D · 1289 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1270 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 347 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 308 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 305 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZJI · PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepin… · the same entry in another collection · chain D against D, TM-score 1.00
- Q13153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 1 (Q13153) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q13153
- Elsewhere: RCSB PDB 4ZJI · PDBe 4ZJI · UniProt Q13153
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