Research workbench
Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety
Analyse Crystal structure of a self-alkylating ribozyme - alkylated form without biotin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJW
- Type
- protein + RNA
- Length
- 999 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Self-alkylating ribozyme (58-mer); Fab havx heavy chain; Fab havx light chain
- Ligands
- 97C
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Self-alkylating ribozyme (58-mer) | rna | 58 | — | — |
| C | Fab havx heavy chain | protein | 227 | 8% helix, 52% strand | — |
| D, L | Fab havx light chain | protein | 214 | 7% helix, 50% strand | — |
| H | Fab havx heavy chain | protein | 228 | 10% helix, 50% strand | — |
Ligands and binding sites
- 97C · 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl pentanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.80 | 0.82 | 83 | empty |
| 2 | 340 | 0.63 | 0.80 | 32 | empty |
| 3 | 317 | 0.58 | 0.77 | 20 | empty |
| 4 | 247 | 0.55 | 0.79 | 18 | empty |
| 5 | 353 | 0.54 | 0.74 | 49 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1908 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1852 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 600 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–L · 591 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 561 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6XJW · Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety · 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
- Elsewhere: RCSB PDB 6XJW · PDBe 6XJW
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