Research workbench
Cryo-EM structure of ST1CAS9-sgrna-TDNA59-ntpam complex.
Analyse Cryo-EM structure of ST1CAS9-sgrna-TDNA59-ntpam complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJD
- Type
- protein + DNA + RNA
- Length
- 954 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptococcus thermophilus 1 CAS9; Sgrna (78-mer); TDNA59; Ntpam
- EC
- 3.1.-.-
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Streptococcus thermophilus 1 CAS9 (EC 3.1.-.-) | protein | 831 | 37% helix, 17% strand | — |
| D | Sgrna (78-mer) | rna | 78 | — | — |
| E | TDNA59 | dna | 32 | — | — |
| G | Ntpam | dna | 13 | — | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.85 | 0.86 | 70 | empty |
| 2 | 897 | 0.80 | 0.83 | 83 | empty |
| 3 | 769 | 0.67 | 0.75 | 47 | empty |
| 4 | 289 | 0.61 | 0.79 | 41 | empty |
| 5 | 288 | 0.58 | 0.78 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 6126 Ų buried · 101 hydrogen bonds · protein-nucleic
- C–E · 1494 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 940 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–G · 604 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–G · 578 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 6RJD · Cryo-EM structure of St1Cas9-sgRNA-tDNA59-ntPAM complex. · the same entry in another collection · chain C against C, 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 6RJD · PDBe 6RJD
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