Research workbench
Crystal structure of human pas kinase bound to ADP
Analyse Crystal structure of human pas kinase bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DLS
- Type
- protein
- Length
- 1,693 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pas domain-containing SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- Q96RG2
- Ligands
- ADP, MG
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 285 | 35% helix, 21% strand | Q96RG2 |
| B | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 280 | 36% helix, 21% strand | Q96RG2 |
| C | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 281 | 35% helix, 19% strand | Q96RG2 |
| D | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 284 | 36% helix, 20% strand | Q96RG2 |
| E | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 282 | 37% helix, 19% strand | Q96RG2 |
| F | Pas domain-containing SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 281 | 35% helix, 19% strand | Q96RG2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 19 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.69 | 0.75 | 83 | MG, ADP |
| 2 | 411 | 0.65 | 0.78 | 52 | MG, ADP |
| 3 | 304 | 0.63 | 0.80 | 38 | MG, ADP |
| 4 | 297 | 0.62 | 0.79 | 35 | MG, ADP |
| 5 | 237 | 0.61 | 0.80 | 35 | MG, ADP |
Interfaces
10 interfaces between chains.
- A–C · 596 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 591 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 568 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 161 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3DLS · Crystal structure of human PAS kinase bound to ADP · the same entry in another collection · chain F against F, TM-score 1.00
- Q96RG2 · AlphaFold monomer V2.0 prediction for pas domain-containing SERINE/THREONINE-protein… · a predicted model of the same protein · chain A 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 Q96RG2
- Elsewhere: RCSB PDB 3DLS · PDBe 3DLS · UniProt Q96RG2
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