Research workbench
Crsytal structure of streptococcus thermophilus CAS9 in complex with the ggaa pam
Analyse Crsytal structure of streptococcus thermophilus CAS9 in complex with the ggaa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M0V
- Type
- protein + DNA + RNA
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (71-mer); DNA (28-mer); DNA (5'-D(*AP*AP*GP*GP*AP*AP*GP*C)-3'); CRISPR-associated…
- EC
- 3.1.-.-
- UniProt
- Q03LF7
- Ligands
- BA, MG
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (71-mer) | rna | 70 | — | — |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (5'-D(*AP*AP*GP*GP*AP*AP*GP*C)-3') | dna | 8 | — | — |
| A | CRISPR-associated endonuclease CAS9 1 (EC 3.1.-.-) | protein | 1030 | 42% helix, 17% strand | Q03LF7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.85 | 0.90 | 59 | BA |
| 2 | 525 | 0.82 | 0.88 | 60 | BA |
| 3 | 784 | 0.80 | 0.84 | 57 | BA |
| 4 | 135 | 0.66 | 0.89 | 23 | empty |
| 5 | 302 | 0.65 | 0.81 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–A · 6404 Ų buried · 177 hydrogen bonds · protein-nucleic
- C–A · 2603 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–C · 1008 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- D–A · 723 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 349 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 6M0V · Crsytal structure of streptococcus thermophilus Cas9 in complex with the GGAA PAM · the same entry in another collection · chain B against B, TM-score 1.00
- Q03LF7 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 1 (Q03LF7) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q03LF7
- Elsewhere: RCSB PDB 6M0V · PDBe 6M0V · UniProt Q03LF7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.