MolNFT v1 · #188408 · protein + DNA + RNA
Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid
7TQB · Fab S9.6 heavy chain: “Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid”. X-ray diffraction, 6 pockets (best druggability 0.58). MolNFT v1 #188408 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TQB
- Type
- protein + DNA + RNA
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab S9.6 heavy chain; Fab S9.6 light chain; RNA; DNA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab S9.6 heavy chain | protein | 208 | 4% helix, 51% strand | — |
| L | Fab S9.6 light chain | protein | 216 | 6% helix, 49% strand | — |
| A | RNA | rna | 13 | — | — |
| B | DNA | dna | 13 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.58 | 0.75 | 54 | empty |
| 2 | 66 | 0.37 | 0.78 | 13 | GOL |
| 3 | 99 | 0.35 | 0.74 | 26 | empty |
| 4 | 56 | 0.29 | 0.75 | 19 | empty |
| 5 | 55 | 0.28 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1882 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- H–A · 375 Ų buried · 11 hydrogen bonds · protein-nucleic
- H–B · 364 Ų buried · 6 hydrogen bonds · protein-nucleic
- L–A · 118 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7TQB · Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 7TQB · PDBe 7TQB
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