MolNFT v1 · #134820 · protein
Structure of the hetero-trimer of RTT102-ARP7/9 bound to ATP
5TGC · Actin-related protein 7: “Structure of the hetero-trimer of RTT102-ARP7/9 bound to ATP”. X-ray diffraction, 2 ligands (ATP, SO4), 15 pockets (best druggability 0.87). MolNFT v1 #134820 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TGC
- Type
- protein
- Length
- 1,750 residues
- Chains
- 6
- 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…
- UniProt
- Q12406, Q05123, P53330
- Ligands
- ATP, SO4
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-related protein 7 | protein | 407 | 46% helix, 19% strand | Q12406 |
| B | Actin-like protein ARP9 | protein | 395 | 40% helix, 19% strand | Q05123 |
| C | Regulator of TY1 transposition protein 102 | protein | 67 | 10% helix, 22% strand | P53330 |
| D | Actin-related protein 7 | protein | 428 | 45% helix, 19% strand | Q12406 |
| E | Actin-like protein ARP9 | protein | 391 | 41% helix, 20% strand | Q05123 |
| F | Regulator of TY1 transposition protein 102 | protein | 62 | 18% helix, 23% strand | P53330 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.87 | 0.91 | 108 | ATP |
| 2 | 951 | 0.86 | 0.88 | 119 | ATP |
| 3 | 575 | 0.86 | 0.91 | 70 | empty |
| 4 | 728 | 0.83 | 0.86 | 78 | empty |
| 5 | 459 | 0.71 | 0.81 | 34 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1951 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1630 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1614 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1575 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1474 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5TGC · Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.97
- Q05123 · AlphaFold monomer V2.0 prediction for actin-like protein ARP9 (Q05123) · a predicted model of the same protein · chain E against A, TM-score 0.96
- P53330 · AlphaFold monomer V2.0 prediction for regulator of TY1 transposition protein 102 (P53330) · a predicted model of the same protein · chain C against A, TM-score 0.47
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 P53330
- Elsewhere: RCSB PDB 5TGC · PDBe 5TGC · UniProt Q12406 · UniProt Q05123 · UniProt P53330
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