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Crystal structure of a CRISPR RNA-guided surveillance complex, cascade, bound to a ssdna target

Analyse Crystal structure of a CRISPR RNA-guided surveillance complex, cascade, bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QYZ
Type: protein + DNA + RNA
Length: 3,241 residues
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR system cascade subunit casa; CRISPR system cascade subunit casb; CRISPR system…
EC: 3.1.-.-
UniProt: Q46901, P76632, Q46899, Q46898, Q46897
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 12 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR system cascade subunit casa	protein	468	44% helix, 15% strand	Q46901
B, C	CRISPR system cascade subunit casb	protein	150	67% helix, 3% strand	P76632
D	CRISPR system cascade subunit casc	protein	340	41% helix, 19% strand	Q46899
E	CRISPR system cascade subunit casc	protein	361	39% helix, 24% strand	Q46899
F	CRISPR system cascade subunit casc	protein	362	40% helix, 26% strand	Q46899
G	CRISPR system cascade subunit casc	protein	360	39% helix, 24% strand	Q46899
H	CRISPR system cascade subunit casc	protein	359	40% helix, 26% strand	Q46899
I	CRISPR system cascade subunit casc	protein	256	32% helix, 29% strand	Q46899
J	CRISPR system cascade subunit casd	protein	195	18% helix, 35% strand	Q46898
K	CRISPR system cascade subunit case (EC 3.1.-.-)	protein	152	24% helix, 37% strand	Q46897
L	RNA (55-mer)	rna	55	—	—
M	DNA (33-mer)	dna	33	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1015	0.87	0.88	99	empty
2	1093	0.84	0.86	98	empty
3	853	0.82	0.84	87	empty
4	452	0.77	0.85	42	empty
5	880	0.74	0.78	71	empty

Interfaces

42 interfaces between chains.

E–F · 1963 Å² buried · 32 hydrogen bonds · protein-protein
H–I · 1954 Å² buried · 35 hydrogen bonds · protein-protein
F–G · 1945 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 1928 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 1923 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4QYZ · Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA… · the same entry in another collection · chain H against H, 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
Every structure of UniProt Q46901
Every structure of UniProt P76632
Every structure of UniProt Q46899
Every structure of UniProt Q46898
Every structure of UniProt Q46897
Elsewhere: RCSB PDB 4QYZ · PDBe 4QYZ · UniProt Q46901 · UniProt P76632 · UniProt Q46899 · UniProt Q46898 · UniProt Q46897

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