Research workbench
Structure of the yeast ckm
Analyse Structure of the yeast ckm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KPX
- Type
- protein
- Length
- 2,875 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meiotic mRNA stability protein kinase SSN3; RNA polymerase II holoenzyme cyclin-like…
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P39073, P47821, P25648, P38931
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meiotic mRNA stability protein kinase SSN3 (EC 2.7.11.22, 2.7.11.23) | protein | 357 | 27% helix, 10% strand | P39073 |
| B | RNA polymerase II holoenzyme cyclin-like subunit | protein | 290 | 57% helix, 0% strand | P47821 |
| C | Mediator of RNA polymerase II transcription subunit 12 | protein | 1352 | 62% helix, 1% strand | P25648 |
| D | Mediator of RNA polymerase II transcription subunit 13 | protein | 876 | 25% helix, 22% strand | P38931 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.82 | 0.83 | 111 | empty |
| 2 | 869 | 0.80 | 0.83 | 121 | empty |
| 3 | 1129 | 0.77 | 0.79 | 85 | empty |
| 4 | 95 | 0.73 | 0.96 | 23 | empty |
| 5 | 991 | 0.73 | 0.77 | 111 | empty |
Interfaces
5 interfaces between chains.
- C–D · 5579 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2754 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2177 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1422 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KPX · Structure of the yeast CKM · the same entry in another collection · chain D against D, TM-score 1.00
- P47821 · AlphaFold monomer V2.0 prediction for RNA polymerase II holoenzyme cyclin-like subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97
- P38931 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain D against A, TM-score 0.96
- P39073 · AlphaFold monomer V2.0 prediction for meiotic mRNA stability protein kinase SSN3 (P39073) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P25648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.72
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 P39073
- Every structure of UniProt P47821
- Every structure of UniProt P25648
- Every structure of UniProt P38931
- Elsewhere: RCSB PDB 7KPX · PDBe 7KPX · UniProt P39073 · UniProt P47821 · UniProt P25648 · UniProt P38931
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