MolNFT v1 · #154474 · protein + DNA + RNA
Crystal structure of wt NME1CAS9 in complex with sgrna and target DNA (atatgatt pam) in post-cleavage state
6KC8 · CRISPR-associated endonuclease CAS9: “Crystal structure of wt NME1CAS9 in complex with sgrna and target DNA (atatgatt pam) in post-cleavage state”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #154474 on…
- PDB
- 6KC8
- Type
- protein + DNA + RNA
- Length
- 1,212 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Sgrna; DNA (5'…
- EC
- 3.1.-.-
- UniProt
- C9X1G5
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1036 | 37% helix, 16% strand | C9X1G5 |
| B | Sgrna | rna | 130 | — | — |
| C | DNA (5'- D(P*AP*AP*GP*TP*TP*AP*AP*AP*TP*AP*GP*CP*AP*GP*AP*GP*TP*GP*AP*CP*C)- 3') | dna | 21 | — | — |
| D | DNA (5'-D(*AP*TP*AP*TP*GP*AP*TP*TP*TP*TP*A)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*TP*AP*AP*AP*AP*TP*CP*AP*TP*AP*TP*GP*TP*A)-3') | dna | 14 | — | — |
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 | 679 | 0.86 | 0.90 | 59 | empty |
| 2 | 522 | 0.84 | 0.90 | 59 | empty |
| 3 | 888 | 0.81 | 0.84 | 70 | empty |
| 4 | 244 | 0.76 | 0.90 | 29 | empty |
| 5 | 439 | 0.75 | 0.85 | 39 | empty |
Interfaces
8 interfaces between chains.
- A–B · 6961 Ų buried · 155 hydrogen bonds · protein-nucleic
- A–C · 1968 Ų buried · 38 hydrogen bonds · protein-nucleic
- B–C · 1003 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–P · 672 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 631 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6KC8 · Crystal structure of WT 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 0.81
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 6KC8 · PDBe 6KC8 · UniProt C9X1G5
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