Research workbench
Human PDK1 kinase domain in complex with an hm-peptide bound to the pif-pocket
Analyse Human PDK1 kinase domain in complex with an hm-peptide bound to the pif-pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LVP
- Type
- protein
- Length
- 1,135 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1; Hydrophobic-motif peptide of PKB/AKT
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- ATP, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 276 | 41% helix, 18% strand | O15530 |
| B | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 277 | 40% helix, 17% strand | O15530 |
| D | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 277 | 42% helix, 18% strand | O15530 |
| E | Hydrophobic-motif peptide of PKB/AKT | protein | 6 | 0% helix, 0% strand | — |
| F, G | Hydrophobic-motif peptide of PKB/AKT | protein | 8 | 0% helix, 13% strand | — |
| H | Hydrophobic-motif peptide of PKB/AKT | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.80 | 0.81 | 74 | CL |
| 2 | 1002 | 0.75 | 0.78 | 44 | CL |
| 3 | 316 | 0.63 | 0.79 | 30 | ATP |
| 4 | 293 | 0.63 | 0.80 | 33 | ATP |
| 5 | 379 | 0.62 | 0.77 | 35 | ATP |
Interfaces
9 interfaces between chains.
- C–D · 781 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 714 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 586 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 565 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 561 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 5LVP · Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket · 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 O15530
- Elsewhere: RCSB PDB 5LVP · PDBe 5LVP · UniProt O15530
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