MolNFT v1 · #122030 · protein + RNA

Structure of CPF1/RNA complex

5ID6: “Structure of CPF1/RNA complex”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.70). MolNFT v1 #122030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ID6
Type: protein + RNA
Length: 1,230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CPF1; RNA (5'- R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)- 3')
Ligands: MG
Pockets: 12 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CPF1	protein	1209	47% helix, 13% strand	—
G	RNA (5'- R(PAPAPUPUPUPCPUPAPCPUPAPAPGPUPGPUPAPGPAPUP*C)- 3')	rna	21	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, G

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.70	0.78	53	empty
2	682	0.68	0.77	63	empty
3	327	0.62	0.79	35	MG
4	245	0.50	0.75	37	empty
5	121	0.49	0.79	15	empty

Interfaces

1 interface between chains.

A–G · 2614 Å² buried · 54 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 19 modified (engineered).

Compared structures

5ID6 · Structure of Cpf1/RNA Complex · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 5ID6 · PDBe 5ID6

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