MolNFT v1 · #179196 · protein + DNA
Analysis of a strand exchange reaction with a mini filament of 9-reca, OLIGO(DT)27 primary ssdna, non-homologous 120 bp dsdna and atpgammas
7JY6 · Protein reca: “Analysis of a strand exchange reaction with a mini filament of 9-reca, OLIGO(DT)27 primary ssdna…”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.87). MolNFT v1 #179196 on GenesisL1: 3D…
- PDB
- 7JY6
- Type
- protein + DNA
- Length
- 3,036 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein reca; DNA (27-mer); DNA (45-mer)
- UniProt
- A0A376NU07
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Protein reca | protein | 333 | 38% helix, 25% strand | A0A376NU07 |
| I | Protein reca | protein | 300 | 36% helix, 26% strand | A0A376NU07 |
| S | DNA (27-mer) | dna | 27 | — | — |
| U | DNA (45-mer) | dna | 45 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.87 | 0.89 | 73 | MG, AGS |
| 2 | 842 | 0.86 | 0.89 | 79 | MG, AGS |
| 3 | 1147 | 0.86 | 0.87 | 82 | MG, AGS |
| 4 | 1128 | 0.85 | 0.86 | 82 | MG, AGS |
| 5 | 1160 | 0.85 | 0.86 | 83 | MG, AGS |
Interfaces
33 interfaces between chains.
- H–I · 2215 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2202 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 2193 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2191 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2174 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7JY6 · Analysis of a strand exchange reaction with a mini filament of 9-RecA, oligo(dT)27… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A376NU07
- Elsewhere: RCSB PDB 7JY6 · PDBe 7JY6 · UniProt A0A376NU07
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