MolNFT v1 · #120723 · protein + DNA + RNA

Crystal structure of E. COLI cascade bound to a pam-containing dsdna target (32-nt spacer) at 3.20 ångström resolution.

5H9E · CRISPR system cascade subunit casa: “Crystal structure of E. COLI cascade bound to a pam-containing dsdna target (32-nt spacer) at 3.20 ångström…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1…

PDB: 5H9E
Type: protein + DNA + RNA
Length: 3,350 residues
Chains: 14
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 0.85

Structure

x-ray diffraction · 14 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR system cascade subunit casa	protein	481	43% helix, 15% strand	Q46901
B	CRISPR system cascade subunit casb	protein	151	68% helix, 3% strand	P76632
C	CRISPR system cascade subunit casb	protein	150	68% helix, 3% strand	P76632
D	CRISPR system cascade subunit casc	protein	318	42% helix, 18% strand	Q46899
E	CRISPR system cascade subunit casc	protein	354	38% helix, 20% strand	Q46899
F	CRISPR system cascade subunit casc	protein	361	39% helix, 24% strand	Q46899
G	CRISPR system cascade subunit casc	protein	354	38% helix, 24% strand	Q46899
H	CRISPR system cascade subunit casc	protein	352	38% helix, 23% strand	Q46899
I	CRISPR system cascade subunit casc	protein	351	40% helix, 21% strand	Q46899
J	CRISPR system cascade subunit casd	protein	219	16% helix, 43% strand	Q46898
L	Crrna (61-mer)	rna	61	—	—
M	DNA (47-mer) non-target	dna	19	—	—
N	DNA (47-mer) target	dna	40	—	—
K	CRISPR system cascade subunit case (EC 3.1.-.-)	protein	139	22% helix, 28% strand	Q46897

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	1181	0.85	0.86	108	empty
2	886	0.84	0.86	116	empty
3	767	0.83	0.87	78	empty
4	1036	0.81	0.83	123	empty
5	555	0.79	0.85	69	empty

Interfaces

45 interfaces between chains.

I–J · 2159 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1978 Å² buried · 35 hydrogen bonds · protein-protein
A–J · 1922 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 1915 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 1903 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5H9E · Crystal structure of E. coli Cascade bound to a PAM-containing dsDNA target (32-nt… · 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 Q46901
Every structure of UniProt P76632
Every structure of UniProt Q46899
Every structure of UniProt Q46898
Every structure of UniProt Q46897
Elsewhere: RCSB PDB 5H9E · PDBe 5H9E · UniProt Q46901 · UniProt P76632 · UniProt Q46899 · UniProt Q46898 · UniProt Q46897

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