MolNFT v1 · #114272 · protein

CAS3-ACRF3 complex

5B7I · CRISPR-associated NUCLEASE/HELICASE CAS3 subtype I-F/YPEST: “CAS3-ACRF3 complex”. X-ray diffraction, 2 ligands (ADP, CA), 16 pockets (best druggability 0.88). MolNFT v1 #114272 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5B7I
Type: protein
Length: 1,319 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated NUCLEASE/HELICASE CAS3 subtype I-F/YPEST; Uncharacterized protein ACRF3
EC: 3.1.-.-, 3.6.4.-
UniProt: Q02ML8, L7P7R7
Ligands: ADP, CA
Pockets: 16 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated NUCLEASE/HELICASE CAS3 subtype I-F/YPEST (EC 3.1.-.-, 3.6.4.-)	protein	1044	42% helix, 15% strand	Q02ML8
B	Uncharacterized protein ACRF3	protein	137	61% helix, 0% strand	L7P7R7
C	Uncharacterized protein ACRF3	protein	138	67% helix, 0% strand	L7P7R7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.88	0.89	125	empty
2	284	0.69	0.84	47	ADP
3	227	0.68	0.85	50	empty
4	224	0.67	0.85	40	empty
5	190	0.65	0.85	36	empty

Interfaces

3 interfaces between chains.

A–C · 1498 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1165 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1106 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 modified (engineered).

Compared structures

5B7I · Cas3-AcrF3 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q02ML8 · AlphaFold monomer V2.0 prediction for CRISPR-associated NUCLEASE/HELICASE CAS3 subtype… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q02ML8
Every structure of UniProt L7P7R7
Elsewhere: RCSB PDB 5B7I · PDBe 5B7I · UniProt Q02ML8 · UniProt L7P7R7

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