MolNFT v1 · #158565 · protein + DNA + RNA

Casx-grna-DNA(30BP) state II

6NY1: “Casx-grna-DNA(30BP) state II”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #158565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NY1
Type: protein + DNA + RNA
Length: 1,057 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Casx; DNA non-target strand; Grna; DNA target strand
UniProt: A0A357BT59
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 4 distinct chains · 35% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Y	Casx	protein	903	35% helix, 8% strand	A0A357BT59
D	DNA non-target strand	dna	17	—	—
B	Grna	rna	108	—	—
C	DNA target strand	dna	29	—	—

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	946	0.79	0.82	72	empty
2	1045	0.77	0.80	51	empty
3	933	0.77	0.80	107	empty
4	1191	0.76	0.79	101	empty
5	143	0.73	0.92	25	empty

Interfaces

5 interfaces between chains.

Y–B · 4252 Å² buried · 65 hydrogen bonds · protein-nucleic
Y–C · 1601 Å² buried · 23 hydrogen bonds · protein-nucleic
B–C · 930 Å² buried · 60 hydrogen bonds · nucleic-nucleic
Y–D · 924 Å² buried · 14 hydrogen bonds · protein-nucleic
D–C · 466 Å² buried · 33 hydrogen bonds · nucleic-nucleic

Compared structures

6NY1 · CasX-gRNA-DNA(30bp) State II · the same entry in another collection · chain Y against Y, 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
Every structure of UniProt A0A357BT59
Elsewhere: RCSB PDB 6NY1 · PDBe 6NY1 · UniProt A0A357BT59

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