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Crystal structure of LBACAS13A (C2C2) bound to mature crrna (24-nt spacer)

Analyse Crystal structure of LBACAS13A (C2C2) bound to mature crrna (24-nt spacer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W1H
Type: protein + RNA
Length: 1,342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LBACAS13A (C2C2); Mature crrna
Ligands: IOD
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LBACAS13A (C2C2)	protein	1301	57% helix, 8% strand	—
B	Mature crrna	rna	41	—	—

Ligands and binding sites

IOD · Iodide ion · ion · 23 copies · chains A
GOL · Glycerol · additive · 3 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	985	0.88	0.90	87	IOD
2	170	0.82	0.97	25	empty
3	135	0.79	0.97	28	empty
4	770	0.78	0.82	67	IOD
5	337	0.77	0.88	48	empty

Interfaces

1 interface between chains.

A–B · 5753 Å² buried · 128 hydrogen bonds · protein-nucleic

Compared structures

5W1H · Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (24-nt spacer) · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5W1H · PDBe 5W1H

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