Research workbench
Plk-1 polo-box domain in complex with a high affinity macrocycle synthesized using a novel glutamic acid analog
Analyse Plk-1 polo-box domain in complex with a high affinity macrocycle synthesized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MX1
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; ACE-pro-leu-ala-ser-tpo
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- ACE, ZOY
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 220 | 31% helix, 30% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 222 | 31% helix, 29% strand | P53350 |
| C, E | ACE-pro-leu-ala-ser-tpo | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, E
- ZOY · N-[(4S)-4,5-diamino-5-oxopentyl]-10-phenyldecanamide · ligand · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.64 | 0.75 | 63 | empty |
| 2 | 51 | 0.42 | 0.83 | 14 | empty |
| 3 | 56 | 0.41 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 434 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 421 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 143 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 7MX1 · PLK-1 polo-box domain in complex with a high affinity macrocycle synthesized using a… · 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 P53350
- Elsewhere: RCSB PDB 7MX1 · PDBe 7MX1 · UniProt P53350
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