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Crystal structure of NME1CAS9-sgrna dimer mediated by double protein inhibitor ACRIIC3 monomers

Analyse Crystal structure of NME1CAS9-sgrna dimer mediated by double protein inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JE9
Type: protein + RNA
Length: 2,554 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated endonuclease CAS9; Sgrna; ACRIIC3
EC: 3.1.-.-
UniProt: C9X1G5, A0A3E2QDI5
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated endonuclease CAS9 (EC 3.1.-.-)	protein	1056	40% helix, 15% strand	C9X1G5
B	Sgrna	rna	115	—	—
C	CRISPR-associated endonuclease CAS9 (EC 3.1.-.-)	protein	1036	41% helix, 16% strand	C9X1G5
D	Sgrna	rna	113	—	—
E, F	ACRIIC3	protein	117	46% helix, 25% strand	A0A3E2QDI5

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.84	0.85	69	empty
2	847	0.82	0.85	60	empty
3	480	0.77	0.86	52	empty
4	1059	0.77	0.80	69	empty
5	701	0.76	0.82	45	empty

Interfaces

6 interfaces between chains.

A–B · 5479 Å² buried · 113 hydrogen bonds · protein-nucleic
C–D · 5269 Å² buried · 109 hydrogen bonds · protein-nucleic
A–F · 963 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 940 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 755 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6JE9 · Crystal structure of Nme1Cas9-sgRNA dimer mediated by double protein inhibitor AcrIIC3… · the same entry in another collection · chain F against F, 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 0.89

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
Every structure of UniProt A0A3E2QDI5
Elsewhere: RCSB PDB 6JE9 · PDBe 6JE9 · UniProt C9X1G5 · UniProt A0A3E2QDI5

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