Research workbench
Near-atomic cryo-EM structure of PRC1 bound to the microtubule
Analyse Near-atomic cryo-EM structure of PRC1 bound to the microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KMG
- Type
- protein
- Length
- 990 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Homo sapiens; Sus scrofa
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Protein regulator of cytokinesis 1
- UniProt
- Q2XVP4, P02554, O43663
- Ligands
- GTP, GDP, POU, MG
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · resolution 3.5 · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 431 | 45% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 431 | 47% helix, 20% strand | P02554 |
| P | Protein regulator of cytokinesis 1 | protein | 128 | 83% helix, 3% strand | O43663 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- POU · Peloruside A · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.84 | 0.95 | 50 | GTP, MG |
| 2 | 306 | 0.62 | 0.80 | 29 | empty |
| 3 | 438 | 0.59 | 0.75 | 42 | empty |
| 4 | 297 | 0.57 | 0.77 | 34 | empty |
| 5 | 189 | 0.54 | 0.79 | 41 | GDP |
Interfaces
3 interfaces between chains.
- A–B · 1995 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 741 Ų buried · 8 hydrogen bonds · protein-protein
- B–P · 440 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KMG · Near-atomic cryo-EM structure of PRC1 bound to the microtubule · the same entry in another collection · chain A against A, TM-score 1.00
- Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02554 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02554) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O43663 · AlphaFold monomer V2.0 prediction for protein regulator of cytokinesis 1 (O43663) · a predicted model of the same protein · chain P against A, TM-score 0.79
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 Q2XVP4
- Every structure of UniProt P02554
- Every structure of UniProt O43663
- Elsewhere: RCSB PDB 5KMG · PDBe 5KMG · UniProt Q2XVP4 · UniProt P02554 · UniProt O43663
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