MolNFT v1 · #119244 · protein + DNA + RNA

Crystal structure of CAS9-sgrna-DNA complex solved by native sad phasing

5FQ5: “Crystal structure of CAS9-sgrna-DNA complex solved by native sad phasing”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.83). MolNFT v1 #119244 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FQ5
Type: protein + DNA + RNA
Length: 1,435 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand proximal fragment…
EC: 3.1.-.-
UniProt: Q99ZW2
Ligands: K, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sgrna	rna	81	—	—
B	CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-)	protein	1318	49% helix, 12% strand	Q99ZW2
C	Target DNA strand proximal fragment	dna	9	—	—
D	Non-target DNA strand	dna	10	—	—
E	Target DNA strand distal fragment	dna	17	—	—

Ligands and binding sites

K · Potassium ion · metal · 13 copies · chains A, E, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.83	0.85	97	MG, K
2	946	0.81	0.83	76	K
3	910	0.77	0.80	95	empty
4	966	0.71	0.76	80	K
5	96	0.68	0.92	24	empty

Interfaces

6 interfaces between chains.

A–B · 6032 Å² buried · 132 hydrogen bonds · protein-nucleic
B–E · 1225 Å² buried · 16 hydrogen bonds · protein-nucleic
A–E · 826 Å² buried · 56 hydrogen bonds · nucleic-nucleic
B–D · 563 Å² buried · 13 hydrogen bonds · protein-nucleic
C–D · 435 Å² buried · 31 hydrogen bonds · nucleic-nucleic

Compared structures

5FQ5 · Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing · the same entry in another collection · chain A against A, TM-score 1.00
Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q99ZW2
Elsewhere: RCSB PDB 5FQ5 · PDBe 5FQ5 · UniProt Q99ZW2

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