Research workbench

Type I-F CRISPR-csy complex with its inhibitor ACRF8

Analyse Type I-F CRISPR-csy complex with its inhibitor ACRF8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VQW
Type: protein + RNA
Length: 2,688 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type I-F CRISPR-associated protein CSY2; CRISPR-associated protein CSY3…
EC: 3.1.-.-
UniProt: B3G161, A0A444M080, Q02MM2, Q02ML9
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 11 distinct chains · 22% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Type I-F CRISPR-associated protein CSY2	protein	297	18% helix, 21% strand	B3G161
D	CRISPR-associated protein CSY3	protein	293	26% helix, 22% strand	A0A444M080
E	CRISPR-associated protein CSY3	protein	333	21% helix, 21% strand	A0A444M080
F	CRISPR-associated protein CSY3	protein	334	23% helix, 23% strand	A0A444M080
G	CRISPR-associated protein CSY3	protein	331	19% helix, 18% strand	A0A444M080
H	CRISPR-associated protein CSY3	protein	325	23% helix, 22% strand	A0A444M080
I	CRISPR-associated protein CSY3	protein	326	23% helix, 22% strand	A0A444M080
J	CRISPR-associated endonuclease CAS6/CSY4 (EC 3.1.-.-)	protein	87	17% helix, 5% strand	Q02MM2
A	ACRF8	protein	80	8% helix, 8% strand	—
B	CRISPR-associated protein CSY1	protein	242	34% helix, 7% strand	Q02ML9
K	Crrna (40-mer)	rna	40	—	—

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	862	0.80	0.83	82	empty
2	1058	0.79	0.81	88	empty
3	926	0.78	0.81	90	empty
4	903	0.76	0.79	94	empty
5	665	0.76	0.82	71	empty

Interfaces

30 interfaces between chains.

C–B · 2850 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 2068 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 2062 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 2035 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 2008 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6VQW · Type I-F CRISPR-Csy complex with its inhibitor AcrF8 · the same entry in another collection · chain K against K, TM-score 1.00
Q02MM2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS6/CSY4 (Q02MM2) · a predicted model of the same protein · chain J against A, TM-score 0.76

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 B3G161
Every structure of UniProt A0A444M080
Every structure of UniProt Q02MM2
Every structure of UniProt Q02ML9
Elsewhere: RCSB PDB 6VQW · PDBe 6VQW · UniProt B3G161 · UniProt A0A444M080 · UniProt Q02MM2 · UniProt Q02ML9

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