Research workbench

CRISPR RNA-guided surveillance complex, pre-nicking

Analyse CRISPR RNA-guided surveillance complex, pre-nicking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C66
Type: protein + DNA + RNA
Length: 4,416 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated helicase, CAS3 family; CRISPR-associated protein, CSE1 family…
UniProt: Q47PJ0, Q47PJ1, Q47PJ3, Q47PJ2, Q47PJ4, Q47PJ5
Ligands: FE
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 13 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	CRISPR-associated helicase, CAS3 family	protein	832	42% helix, 12% strand	Q47PJ0
A	CRISPR-associated protein, CSE1 family	protein	511	36% helix, 14% strand	Q47PJ1
B	CRISPR-associated protein, CSE4 family	protein	334	25% helix, 22% strand	Q47PJ3
C, D	CRISPR-associated protein, CSE4 family	protein	367	35% helix, 22% strand	Q47PJ3
E, F	CRISPR-associated protein, CSE4 family	protein	366	36% helix, 21% strand	Q47PJ3
H	CRISPR-associated protein, CSE4 family	protein	329	40% helix, 19% strand	Q47PJ3
I	Uncharacterized protein	protein	177	72% helix, 0% strand	Q47PJ2
J	Crrna	rna	59	—	—
K	Uncharacterized protein	protein	165	79% helix, 0% strand	Q47PJ2
L	Target strand	dna	50	—	—
M	CRISPR-associated protein, CAS5E family	protein	244	19% helix, 32% strand	Q47PJ4
N	Nontarget strand	dna	37	—	—
O	CRISPR-associated protein, CSE3 family	protein	212	17% helix, 23% strand	Q47PJ5

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains G, N

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	1033	0.85	0.86	87	empty
2	1102	0.85	0.86	93	empty
3	702	0.84	0.88	78	empty
4	1150	0.84	0.85	101	empty
5	1019	0.82	0.84	112	empty

Interfaces

55 interfaces between chains.

G–A · 2593 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2259 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 2229 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2178 Å² buried · 28 hydrogen bonds · protein-protein
C–H · 2146 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6C66 · CRISPR RNA-guided surveillance complex, pre-nicking · the same entry in another collection · chain G against G, 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 Q47PJ0
Every structure of UniProt Q47PJ1
Every structure of UniProt Q47PJ3
Every structure of UniProt Q47PJ2
Every structure of UniProt Q47PJ4
Every structure of UniProt Q47PJ5
Elsewhere: RCSB PDB 6C66 · PDBe 6C66 · UniProt Q47PJ0 · UniProt Q47PJ1 · UniProt Q47PJ3 · UniProt Q47PJ2 · UniProt Q47PJ4 · UniProt Q47PJ5

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