MolNFT v1 · #179198 · protein + DNA
Analysis of a strand exchange reaction with a mini filament of 9-reca, 27-mer ssdna, partially-homologous 67 bp dsdna and atpgammas
7JY8 · Protein reca: “Analysis of a strand exchange reaction with a mini filament of 9-reca, 27-mer ssdna, partially-homologous 67…”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.80). MolNFT v1 #179198 on…
- PDB
- 7JY8
- Type
- protein + DNA
- Length
- 3,001 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein reca; DNA (27-mer); DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
- UniProt
- A0A376NU07
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Protein reca | protein | 333 | 40% helix, 26% strand | A0A376NU07 |
| I | Protein reca | protein | 300 | 35% helix, 28% strand | A0A376NU07 |
| S | DNA (27-mer) | dna | 27 | — | — |
| T | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 10 | — | — |
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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.80 | 0.82 | 79 | MG, AGS |
| 2 | 836 | 0.79 | 0.82 | 79 | MG, AGS |
| 3 | 925 | 0.79 | 0.81 | 93 | MG, AGS |
| 4 | 898 | 0.79 | 0.81 | 85 | MG, AGS |
| 5 | 800 | 0.79 | 0.82 | 78 | MG, AGS |
Interfaces
30 interfaces between chains.
- A–B · 2245 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2222 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2221 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2214 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 2197 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7JY8 · Analysis of a strand exchange reaction with a mini filament of 9-RecA, 27-mer ssDNA… · 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 7JY8 · PDBe 7JY8 · UniProt A0A376NU07
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.