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Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target DNA (agaaaca pam)

Analyse Crystal structure of campylobacter jejuni CAS9 in complex with sgrna and target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X2H
Type: protein + DNA + RNA
Length: 875 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
UniProt: Q0P897
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated endonuclease CAS9	protein	746	42% helix, 17% strand	Q0P897
B	Sgrna	rna	93	—	—
C	Target DNA strand	dna	28	—	—
D	Non-target DNA strand	dna	8	—	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.79	0.85	71	empty
2	438	0.79	0.87	47	EDO
3	919	0.78	0.81	65	empty
4	846	0.78	0.82	52	empty
5	99	0.78	0.98	21	empty

Interfaces

5 interfaces between chains.

A–B · 5411 Å² buried · 112 hydrogen bonds · protein-nucleic
A–C · 1876 Å² buried · 38 hydrogen bonds · protein-nucleic
B–C · 988 Å² buried · 93 hydrogen bonds · nucleic-nucleic
A–D · 553 Å² buried · 12 hydrogen bonds · protein-nucleic
C–D · 364 Å² buried · 32 hydrogen bonds · nucleic-nucleic

Compared structures

5X2H · Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA… · the same entry in another collection · chain A against A, TM-score 1.00
Q0P897 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (Q0P897) · 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 Q0P897
Elsewhere: RCSB PDB 5X2H · PDBe 5X2H · UniProt Q0P897

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