Research workbench
Crystal structure of a nuclear actin ternary complex
Analyse Crystal structure of a nuclear actin ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I9E
- Type
- protein
- Length
- 1,599 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 4; Actin; Helicase SWR1
- EC
- 3.6.4.12
- UniProt
- P80428, P60011, Q05471
- Ligands
- ATP, MG
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-related protein 4 | protein | 421 | 35% helix, 19% strand | P80428 |
| B | Actin | protein | 351 | 43% helix, 19% strand | P60011 |
| C | Actin-related protein 4 | protein | 404 | 36% helix, 19% strand | P80428 |
| D | Actin | protein | 338 | 46% helix, 17% strand | P60011 |
| H | Helicase SWR1 (EC 3.6.4.12) | protein | 44 | 84% helix, 0% strand | Q05471 |
| E | Helicase SWR1 (EC 3.6.4.12) | protein | 41 | 90% helix, 0% strand | Q05471 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.89 | 0.91 | 129 | ATP, MG |
| 2 | 1186 | 0.88 | 0.90 | 119 | MG, ATP |
| 3 | 364 | 0.79 | 0.89 | 46 | empty |
| 4 | 889 | 0.75 | 0.79 | 95 | empty |
| 5 | 305 | 0.69 | 0.83 | 41 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1415 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1381 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1216 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1057 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 811 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5I9E · Crystal structure of a nuclear actin ternary complex · the same entry in another collection · chain E against E, TM-score 1.00
- P60011 · AlphaFold monomer V2.0 prediction for actin (P60011) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P80428 · AlphaFold monomer V2.0 prediction for actin-related protein 4 (P80428) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q05471 · AlphaFold monomer V2.0 prediction for helicase SWR1 (Q05471) · a predicted model of the same protein · chain E against A, TM-score 0.83
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 P80428
- Every structure of UniProt P60011
- Every structure of UniProt Q05471
- Elsewhere: RCSB PDB 5I9E · PDBe 5I9E · UniProt P80428 · UniProt P60011 · UniProt Q05471
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