MolNFT v2 · #154427 · protein + DNA + RNA
Crystal structure of Nme2Cas9 in complex with sgRNA and target DNA (AGGCCC PAM) with 5 nt overhang
6JE3 · CRISPR-associated endonuclease Cas9: “Crystal structure of Nme2Cas9 in complex with sgRNA and target DNA (AGGCCC PAM) with 5 nt overhang”. X-ray diffraction at 2.931, 20 pockets (best druggability 0.86). MolNFT v2 #154427 on…
- PDB
- 6JE3
- Type
- protein + DNA + RNA
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.931
- Source
- Neisseria meningitidis; SYNTHETIC CONSTRUCT
- Molecule
- CRISPR-associated endonuclease Cas9; sgRNA; target DNA strand; non-target DNA strand
- EC
- 3.1.-.-
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.931 · 4 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease Cas9 (EC 3.1.-.-) | protein | 858 | 37% helix, 13% strand | — |
| B | sgRNA | rna | 117 | — | — |
| C | target DNA strand | dna | 35 | — | — |
| D | non-target DNA strand | dna | 13 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.86 | 0.87 | 135 | empty |
| 2 | 643 | 0.86 | 0.91 | 52 | empty |
| 3 | 383 | 0.80 | 0.90 | 40 | empty |
| 4 | 1115 | 0.76 | 0.78 | 108 | empty |
| 5 | 732 | 0.75 | 0.81 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5739 Ų buried · 138 hydrogen bonds · protein-nucleic
- A–C · 1820 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 1151 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- A–D · 833 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 512 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6JE3 · Crystal structure of NME2CAS9 in complex with sgrna and target DNA (aggccc pam) with 5 nt… · 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 6JE3 · PDBe 6JE3
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