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Crystal structure of FNCAS12A bound to a crrna

Analyse Crystal structure of FNCAS12A bound to a crrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NG6
Type: protein + RNA
Length: 5,147 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated endonuclease CPF1; Crrna
EC: 3.1.-.-
UniProt: A0Q7Q2
Ligands: MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	CRISPR-associated endonuclease CPF1 (EC 3.1.-.-)	protein	1268	47% helix, 13% strand	A0Q7Q2
B, D, F, H	Crrna	rna	24	—	—
E	CRISPR-associated endonuclease CPF1 (EC 3.1.-.-)	protein	1262	47% helix, 13% strand	A0Q7Q2
G	CRISPR-associated endonuclease CPF1 (EC 3.1.-.-)	protein	1253	48% helix, 13% strand	A0Q7Q2

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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	1099	0.77	0.79	83	empty
2	1005	0.76	0.78	82	empty
3	660	0.76	0.81	66	empty
4	753	0.75	0.80	65	empty
5	669	0.75	0.81	73	empty

Interfaces

9 interfaces between chains.

C–D · 2887 Å² buried · 61 hydrogen bonds · protein-nucleic
G–H · 2833 Å² buried · 55 hydrogen bonds · protein-nucleic
A–B · 2809 Å² buried · 57 hydrogen bonds · protein-nucleic
E–F · 2795 Å² buried · 54 hydrogen bonds · protein-nucleic
C–E · 718 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5NG6 · Crystal structure of FnCas12a bound to a crRNA · the same entry in another collection · chain H against H, TM-score 1.00
A0Q7Q2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (A0Q7Q2) · a predicted model of the same protein · chain G against A, TM-score 0.74

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 A0Q7Q2
Elsewhere: RCSB PDB 5NG6 · PDBe 5NG6 · UniProt A0Q7Q2

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