Research workbench

The type ie CRISPR cascade complex from E. COLI, with two assemblies in the asymmetric unit arranged back-to-back

Analyse The type ie CRISPR cascade complex from E. COLI, with two assemblies in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CD4
Type: protein + RNA
Length: 6,840 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR system cascade subunit case; CRISPR system cascade subunit casc; CRISPR system…
EC: 3.1.-.-
UniProt: Q46897, Q46899, Q46898, Q46901, P76632
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 22 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR system cascade subunit case (EC 3.1.-.-)	protein	199	20% helix, 43% strand	Q46897
B	CRISPR system cascade subunit casc	protein	357	41% helix, 18% strand	Q46899
C	CRISPR system cascade subunit casc	protein	356	38% helix, 23% strand	Q46899
D	CRISPR system cascade subunit casc	protein	355	38% helix, 24% strand	Q46899
E	CRISPR system cascade subunit casc	protein	362	38% helix, 23% strand	Q46899
F	CRISPR system cascade subunit casc	protein	363	37% helix, 23% strand	Q46899
G	CRISPR system cascade subunit casc	protein	362	38% helix, 20% strand	Q46899
H, T	CRISPR system cascade subunit casd	protein	219	16% helix, 37% strand	Q46898
I	CRISPR system cascade subunit casa	protein	494	40% helix, 16% strand	Q46901
J	CRISPR system cascade subunit casb	protein	156	63% helix, 3% strand	P76632
K	CRISPR system cascade subunit casb	protein	154	66% helix, 3% strand	P76632
L, X	Crrna	rna	61	—	—
M	CRISPR system cascade subunit case (EC 3.1.-.-)	protein	192	23% helix, 43% strand	Q46897
N	CRISPR system cascade subunit casc	protein	356	40% helix, 19% strand	Q46899
O	CRISPR system cascade subunit casc	protein	351	38% helix, 23% strand	Q46899
P	CRISPR system cascade subunit casc	protein	359	38% helix, 23% strand	Q46899
Q	CRISPR system cascade subunit casc	protein	359	38% helix, 25% strand	Q46899
R	CRISPR system cascade subunit casc	protein	357	39% helix, 23% strand	Q46899
S	CRISPR system cascade subunit casc	protein	353	39% helix, 20% strand	Q46899
U	CRISPR system cascade subunit casa	protein	492	40% helix, 16% strand	Q46901
V	CRISPR system cascade subunit casb	protein	152	65% helix, 3% strand	P76632
W	CRISPR system cascade subunit casb	protein	151	66% helix, 3% strand	P76632

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains I, U

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	965	0.85	0.86	119	empty
2	1199	0.82	0.83	115	empty
3	1042	0.81	0.83	130	empty
4	856	0.79	0.82	105	empty
5	171	0.78	0.94	26	empty

Interfaces

70 interfaces between chains.

S–T · 2220 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2204 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 2023 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1989 Å² buried · 29 hydrogen bonds · protein-protein
R–S · 1975 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 modified (disulfide, nucleotide modification).

Compared structures

5CD4 · The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric… · the same entry in another collection · chain J against J, 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 Q46897
Every structure of UniProt Q46899
Every structure of UniProt Q46898
Every structure of UniProt Q46901
Every structure of UniProt P76632
Elsewhere: RCSB PDB 5CD4 · PDBe 5CD4 · UniProt Q46897 · UniProt Q46899 · UniProt Q46898 · UniProt Q46901 · UniProt P76632

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.