MolNFT v1 · #169678 · protein + RNA
Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate
6XJY · Self-alkylating ribozyme (58-mer): “Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate”. X-ray diffraction, 15 pockets (best druggability 0.69). MolNFT v1 #169678 on GenesisL1: 3D…
- PDB
- 6XJY
- Type
- protein + RNA
- Length
- 994 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
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Self-alkylating ribozyme (58-mer) | rna | 58 | — | — |
| C, H | Fab havx heavy chain | protein | 225 | 7% helix, 50% strand | — |
| D, L | Fab havx light chain | protein | 214 | 6% helix, 50% strand | — |
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.69 | 0.81 | 43 | empty |
| 2 | 448 | 0.69 | 0.81 | 44 | empty |
| 3 | 291 | 0.59 | 0.80 | 16 | empty |
| 4 | 299 | 0.59 | 0.79 | 19 | empty |
| 5 | 345 | 0.54 | 0.74 | 50 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1935 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1922 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 569 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 563 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–H · 551 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6XJY · Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide… · 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 6XJY · PDBe 6XJY
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