MolNFT v1 · #156340 · protein + DNA + RNA
Crsytal structure of streptococcus thermophilus CAS9 in complex with the ggaa pam
6M0V · RNA (71-mer): “Crsytal structure of streptococcus thermophilus CAS9 in complex with the ggaa pam”. X-ray diffraction, 2 ligands (BA, MG), 19 pockets (best druggability 0.85). MolNFT v1 #156340 on GenesisL1: 3D structure, binding…
- 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
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