MolNFT v1 · #179199 · protein + DNA
Structure of a 9 base pair reca-D loop complex
7JY9 · Protein reca: “Structure of a 9 base pair reca-D loop complex”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.87). MolNFT v1 #179199 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JY9
- Type
- protein + DNA
- Length
- 3,075 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein reca; DNA (42-mer); DNA (27-mer)
- UniProt
- A0A376NU07
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 37% 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, 27% strand | A0A376NU07 |
| T | DNA (42-mer) | dna | 42 | — | — |
| U | DNA (42-mer) | dna | 42 | — | — |
| S | DNA (27-mer) | dna | 27 | — | — |
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 | 1123 | 0.87 | 0.88 | 86 | MG, AGS |
| 2 | 1056 | 0.85 | 0.86 | 81 | MG, AGS |
| 3 | 1100 | 0.84 | 0.85 | 84 | MG, AGS |
| 4 | 861 | 0.80 | 0.83 | 73 | MG, AGS |
| 5 | 821 | 0.80 | 0.83 | 78 | MG, AGS |
Interfaces
37 interfaces between chains.
- E–F · 2268 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2264 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2255 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 2240 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2238 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7JY9 · Structure of a 9 base pair RecA-D loop complex · 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 7JY9 · PDBe 7JY9 · UniProt A0A376NU07
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