Research workbench
Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom
Analyse Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8RTY
- Type
- protein
- Length
- 2,424 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 6.25
- Source
- Amanita phalloides; Homo sapiens; Schizosaccharomyces pombe
- Molecule
- Actin, cytoplasmic 1, N-terminally processed; Methylated-DNA--protein-cysteine…
- EC
- 2.1.1.63
- UniProt
- P60709, P16455, Q10059, P07737
- Ligands
- ADP, MG, PO4
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 6.25 · 5 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Actin, cytoplasmic 1, N-terminally processed | protein | 370 | 39% helix, 20% strand | P60709 |
| E | Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12 (EC 2.1.1.63) | protein | 389 | 64% helix, 2% strand | P16455, Q10059 |
| F | Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12 (EC 2.1.1.63) | protein | 395 | 62% helix, 2% strand | P16455, Q10059 |
| H, I, J | Phalloidin (Amanita phalloides) | protein | 7 | 0% helix, 0% strand | — |
| P | Profilin-1 | protein | 139 | 29% helix, 32% strand | P07737 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 843 | 0.86 | 0.88 | 106 | empty |
| 2 | 854 | 0.82 | 0.84 | 89 | empty |
| 3 | 401 | 0.81 | 0.90 | 68 | ADP, MG, PO4 |
| 4 | 435 | 0.81 | 0.89 | 55 | ADP, MG |
| 5 | 163 | 0.79 | 0.94 | 38 | empty |
Interfaces
20 interfaces between chains.
- E–F · 4012 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1149 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1109 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 825 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 801 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 3 d-amino (methylation, D-amino acid, hydroxylation, nonstandard).
Compared structures
- P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P07737 · AlphaFold monomer V2.0 prediction for profilin-1 (P07737) · a predicted model of the same protein · chain P against A, TM-score 0.97
- Q10059 · AlphaFold monomer V2.0 prediction for cell division control protein 12 (Q10059) · a predicted model of the same protein · chain E against A, TM-score 0.82
- P16455 · AlphaFold monomer V2.0 prediction for methylated-DNA--protein- cysteine methyltransferase… · a predicted model of the same protein · chain E against A, TM-score 0.15
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 P60709
- Every structure of UniProt P16455
- Every structure of UniProt Q10059
- Every structure of UniProt P07737
- Elsewhere: RCSB PDB 8RTY · PDBe 8RTY · UniProt P60709 · UniProt P16455 · UniProt Q10059 · UniProt P07737
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