MolNFT v1 · #142244 · protein

Crystal structure of streptococcus pyogenes type II-a CAS2

5ZYF · CRISPR-associated endoribonuclease CAS2: “Crystal structure of streptococcus pyogenes type II-a CAS2”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.58). MolNFT v1 #142244 on GenesisL1: 3D structure, binding…

PDB: 5ZYF
Type: protein
Length: 500 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated endoribonuclease CAS2
EC: 3.1.-.-
UniProt: Q99ZW0
Ligands: SO4
Pockets: 10 · best druggability 0.58

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	88	40% helix, 33% strand	Q99ZW0
B	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	87	40% helix, 31% strand	Q99ZW0
C	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	83	39% helix, 36% strand	Q99ZW0
D	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	85	35% helix, 34% strand	Q99ZW0
E	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	78	40% helix, 35% strand	Q99ZW0
F	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	79	35% helix, 34% strand	Q99ZW0

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, E, F

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.58	0.78	29	EDO
2	105	0.57	0.85	29	EDO
3	305	0.54	0.75	48	empty
4	176	0.51	0.78	25	empty
5	164	0.50	0.78	24	EDO

Interfaces

7 interfaces between chains.

A–B · 1452 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1287 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1271 Å² buried · 28 hydrogen bonds · protein-protein
C–F · 655 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 627 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5ZYF · Crystal structure of Streptococcus pyogenes type II-A Cas2 · 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
Every structure of UniProt Q99ZW0
Elsewhere: RCSB PDB 5ZYF · PDBe 5ZYF · UniProt Q99ZW0

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