MolNFT v1 · #54654 · protein

SSO1725, a protein involved in the CRISPR/CAS pathway

2XVO: “SSO1725, a protein involved in the CRISPR/CAS pathway”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.77). MolNFT v1 #54654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XVO
Type: protein
Length: 724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SSO1725
UniProt: Q97XK8
Ligands: SO4
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SSO1725	protein	184	12% helix, 46% strand	Q97XK8
B	SSO1725	protein	181	11% helix, 45% strand	Q97XK8
C	SSO1725	protein	180	11% helix, 43% strand	Q97XK8
D	SSO1725	protein	179	11% helix, 46% strand	Q97XK8

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, D
BME · Beta-mercaptoethanol · additive · 3 copies · chains A, C, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.77	0.84	56	empty
2	154	0.48	0.77	26	BME
3	86	0.45	0.80	20	empty
4	114	0.39	0.75	25	BME
5	107	0.38	0.75	17	empty

Interfaces

5 interfaces between chains.

A–C · 976 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 855 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 658 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 343 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 159 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

2XVO · SSO1725, a protein involved in the CRISPR/Cas pathway · the same entry in another collection · chain D against D, TM-score 1.00
Q97XK8 · AlphaFold monomer V2.0 prediction for putative CRISPR system cmr subunit CMR7 2 (Q97XK8) · a predicted model of the same protein · 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 Q97XK8
Elsewhere: RCSB PDB 2XVO · PDBe 2XVO · UniProt Q97XK8

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