Research workbench
Crystal structure of NME1CAS9 in complex with sgrna and target DNA (atatgatt pam) in seed-base paring state
Analyse Crystal structure of NME1CAS9 in complex with sgrna and target DNA (atatgatt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KC7
- Type
- protein + DNA + RNA
- Length
- 1,104 residues
- Chains
- 4
- 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 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 963 | 38% helix, 15% strand | C9X1G5 |
| B | Sgrna | rna | 111 | — | — |
| C | DNA (5'- D(*TP*AP*AP*AP*AP*TP*CP*AP*TP*AP*TP*GP*TP*AP*AP*AP*GP*TP*T)-3') | dna | 19 | — | — |
| D | DNA (5'-D(*AP*TP*AP*TP*GP*AP*TP*TP*TP*TP*A)-3') | dna | 11 | — | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.85 | 0.90 | 55 | empty |
| 2 | 502 | 0.80 | 0.87 | 59 | empty |
| 3 | 441 | 0.76 | 0.86 | 47 | empty |
| 4 | 623 | 0.74 | 0.81 | 42 | empty |
| 5 | 55 | 0.70 | 0.98 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5435 Ų buried · 113 hydrogen bonds · protein-nucleic
- A–C · 1083 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 634 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 480 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- B–C · 406 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 6KC7 · 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 0.94
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 6KC7 · PDBe 6KC7 · UniProt C9X1G5
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