Research workbench

CAS1-CAS2 bound to half-site intermediate

Analyse CAS1-CAS2 bound to half-site intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VVJ
Type: protein + DNA
Length: 1,352 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated endonuclease CAS1; CRISPR-associated endoribonuclease CAS2; DNA…
EC: 3.1.-.-
UniProt: Q46896, P45956
Pockets: 18 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	262	52% helix, 12% strand	Q46896
B	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	269	52% helix, 16% strand	Q46896
C	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	253	55% helix, 13% strand	Q46896
D	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	265	53% helix, 15% strand	Q46896
E	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	93	26% helix, 44% strand	P45956
F	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	95	25% helix, 45% strand	P45956
G	DNA (28-mer)	dna	28	—	—
H	DNA (112-mer)	dna	87	—	—

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1176	0.81	0.83	93	empty
2	1008	0.81	0.82	76	empty
3	698	0.77	0.82	46	empty
4	623	0.74	0.81	64	empty
5	738	0.72	0.79	43	empty

Interfaces

20 interfaces between chains.

A–B · 1761 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 1754 Å² buried · 33 hydrogen bonds · protein-nucleic
C–D · 1696 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1253 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 1039 Å² buried · 73 hydrogen bonds · nucleic-nucleic

Compared structures

5VVJ · Cas1-Cas2 bound to half-site intermediate · the same entry in another collection · chain H against H, TM-score 1.00
Q46896 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS1 (Q46896) · a predicted model of the same protein · chain B against A, TM-score 0.97
P45956 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS2 (P45956) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 Q46896
Every structure of UniProt P45956
Elsewhere: RCSB PDB 5VVJ · PDBe 5VVJ · UniProt Q46896 · UniProt P45956

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