Research workbench
High resolution structure of a specific synthetic Fab bound to P4-P6 RNA ribozyme domain
Analyse High resolution structure of a specific synthetic Fab bound to P4-P6 RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R8S
- Type
- protein + RNA
- Length
- 591 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P4-P6 RNA ribozyme domain; Fab light chain; Fab heavy chain
- Ligands
- MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | P4-P6 RNA ribozyme domain | rna | 159 | — | — |
| L | Fab light chain | protein | 214 | 7% helix, 51% strand | — |
| H | Fab heavy chain | protein | 218 | 8% helix, 51% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.76 | 0.79 | 66 | empty |
| 2 | 330 | 0.61 | 0.79 | 24 | MG |
| 3 | 64 | 0.61 | 0.91 | 16 | empty |
| 4 | 571 | 0.61 | 0.74 | 63 | empty |
| 5 | 393 | 0.53 | 0.74 | 24 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1771 Ų buried · 15 hydrogen bonds · protein-protein
- R–H · 870 Ų buried · 23 hydrogen bonds · protein-nucleic
- R–L · 552 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2R8S · High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain · the same entry in another collection · chain R against R, 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 2R8S · PDBe 2R8S
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.