MolNFT v1 · #153420 · protein + DNA + RNA
Crystal structure of NME1CAS9 in complex with sgrna and target DNA (atatgatt pam) in catalytic state
6JDV · CRISPR-associated endonuclease CAS9: “Crystal structure of NME1CAS9 in complex with sgrna and target DNA (atatgatt pam) in catalytic state”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.86). MolNFT v1 #153420 on…
- PDB
- 6JDV
- Type
- protein + DNA + RNA
- Length
- 1,225 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Sgrna; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- C9X1G5
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1036 | 39% helix, 16% strand | C9X1G5 |
| B | Sgrna | rna | 143 | — | — |
| C | Target DNA strand | dna | 35 | — | — |
| D | Non-target DNA strand | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.86 | 0.91 | 60 | empty |
| 2 | 657 | 0.84 | 0.88 | 84 | EDO |
| 3 | 354 | 0.79 | 0.89 | 36 | empty |
| 4 | 222 | 0.77 | 0.91 | 23 | empty |
| 5 | 216 | 0.75 | 0.90 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 7041 Ų buried · 171 hydrogen bonds · protein-nucleic
- A–C · 2945 Ų buried · 55 hydrogen bonds · protein-nucleic
- B–C · 1137 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–D · 664 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–D · 476 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JDV · Crystal structure of Nme1Cas9 in complex with sgRNA and target DNA (ATATGATT PAM) in… · the same entry in another collection · chain A against A, TM-score 1.00
- C9X1G5 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (C9X1G5) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 C9X1G5
- Elsewhere: RCSB PDB 6JDV · PDBe 6JDV · UniProt C9X1G5
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