MolNFT v1 · #116860 · protein + DNA

Crystal structure of CAS-DNA-10 complex

5DQU · CRISPR-associated endonuclease CAS1: “Crystal structure of CAS-DNA-10 complex”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #116860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DQU
Type: protein + DNA
Length: 1,301 residues
Chains: 10
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: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	260	54% helix, 15% strand	Q46896
E	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	93	26% helix, 46% strand	P45956
D	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	258	53% helix, 16% strand	Q46896
C	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	274	51% helix, 15% strand	Q46896
F	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	92	26% helix, 45% strand	P45956
B	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	270	52% helix, 15% strand	Q46896
H, I	DNA (5'-D(GPAPGPTPCPGPAPTPGPCPTPTPTPTP*T)- 3')	dna	15	—	—
J, G	DNA (5'-D(PTPTPGPCPAPTPCPGPAPCPTPC)-3')	dna	12	—	—

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	931	0.81	0.84	67	empty
2	872	0.80	0.83	56	empty
3	220	0.76	0.90	34	empty
4	225	0.74	0.88	34	empty
5	615	0.69	0.78	34	empty

Interfaces

24 interfaces between chains.

A–B · 1701 Å² buried · 13 hydrogen bonds · protein-protein
D–C · 1689 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1249 Å² buried · 8 hydrogen bonds · protein-protein
D–I · 814 Å² buried · 19 hydrogen bonds · protein-nucleic
A–H · 814 Å² buried · 21 hydrogen bonds · protein-nucleic

Compared structures

5DQU · Crystal Structure of Cas-DNA-10 complex · the same entry in another collection · chain G against G, 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 0.98

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 5DQU · PDBe 5DQU · UniProt Q46896 · UniProt P45956

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