Research workbench
Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSSpTVLI phosphopeptide from BRCA2
Analyse Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSSpTVLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GY2
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.11
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Serine/threonine-protein kinase PLK1; Phosphopeptide of BRCA2
- EC
- 2.7.11.21
- UniProt
- P53350
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · resolution 3.11 · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) | protein | 224 | 33% helix, 29% strand | P53350 |
| B | Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) | protein | 224 | 33% helix, 29% strand | P53350 |
| C, D | Phosphopeptide of BRCA2 | protein | 12 | 0% helix, 25% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.62 | 0.79 | 35 | empty |
| 2 | 102 | 0.47 | 0.80 | 20 | empty |
| 3 | 108 | 0.47 | 0.79 | 23 | empty |
| 4 | 186 | 0.46 | 0.75 | 31 | empty |
| 5 | 60 | 0.37 | 0.78 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–D · 662 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6GY2 · Crystal structure of human PLK1-pbd in complex with wssslatpptlssptvli phosphopeptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P53350 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (P53350) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P53350
- Elsewhere: RCSB PDB 6GY2 · PDBe 6GY2 · UniProt P53350
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