Research workbench
Structure of ARP7-ARP9-SNF2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.
Analyse Structure of ARP7-ARP9-SNF2(HSA)-RTT102 subcomplex of SWI/SNF chromatin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I6M
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 7; Actin-like protein ARP9; Regulator of TY1 transposition protein…
- EC
- 3.6.4.-
- UniProt
- Q12406, Q05123, P22082, P53330
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-related protein 7 | protein | 399 | 46% helix, 19% strand | Q12406 |
| B | Actin-like protein ARP9 | protein | 396 | 40% helix, 19% strand | Q05123 |
| C | Actin-like protein ARP9 (EC 3.6.4.-) | protein | 69 | 94% helix, 0% strand | P22082 |
| D | Regulator of TY1 transposition protein 102 | protein | 54 | 13% helix, 28% strand | P53330 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.88 | 0.90 | 133 | PO4 |
| 2 | 138 | 0.79 | 0.96 | 37 | PO4 |
| 3 | 292 | 0.65 | 0.82 | 40 | PO4 |
| 4 | 254 | 0.60 | 0.80 | 35 | PO4 |
| 5 | 246 | 0.56 | 0.78 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1666 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1014 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 649 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4I6M · Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler. · the same entry in another collection · chain D against D, TM-score 1.00
- Q05123 · AlphaFold monomer V2.0 prediction for actin-like protein ARP9 (Q05123) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q12406 · AlphaFold monomer V2.0 prediction for actin-related protein 7 (Q12406) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P22082 · AlphaFold monomer V2.0 prediction for transcription regulatory protein SNF2 (P22082) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P53330 · AlphaFold monomer V2.0 prediction for regulator of TY1 transposition protein 102 (P53330) · a predicted model of the same protein · chain D against A, TM-score 0.50
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 Q12406
- Every structure of UniProt Q05123
- Every structure of UniProt P22082
- Every structure of UniProt P53330
- Elsewhere: RCSB PDB 4I6M · PDBe 4I6M · UniProt Q12406 · UniProt Q05123 · UniProt P22082 · UniProt P53330
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