MolNFT v1 · #119437 · protein + DNA + RNA

Crystal structure of SPYCAS9 variant vqr bound to sgrna and tgag pam target DNA

5FW1: “Crystal structure of SPYCAS9 variant vqr bound to sgrna and tgag pam target DNA”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.83). MolNFT v1 #119437 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5FW1
Type: protein + DNA + RNA
Length: 1,424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand; Non-target DNA strand
EC: 3.1.-.-
UniProt: Q99ZW2
Ligands: K, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 50% 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	1304	50% helix, 12% strand	Q99ZW2
C	Target DNA strand	dna	28	—	—
D	Non-target DNA strand	dna	11	—	—

Ligands and binding sites

K · Potassium ion · metal · 13 copies · chains A, C, B, D
MG · Magnesium ion · metal · 2 copies · 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.83	0.85	111	K, MG
2	672	0.77	0.83	52	empty
3	766	0.72	0.79	53	empty
4	318	0.66	0.82	33	empty
5	303	0.65	0.81	47	K

Interfaces

5 interfaces between chains.

A–B · 6055 Å² buried · 141 hydrogen bonds · protein-nucleic
B–C · 1734 Å² buried · 22 hydrogen bonds · protein-nucleic
A–C · 970 Å² buried · 69 hydrogen bonds · nucleic-nucleic
B–D · 631 Å² buried · 18 hydrogen bonds · protein-nucleic
C–D · 386 Å² buried · 23 hydrogen bonds · nucleic-nucleic

Compared structures

5FW1 · Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA · 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 5FW1 · PDBe 5FW1 · UniProt Q99ZW2

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