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Crystal structure of CRISPR associated protein

Analyse Crystal structure of CRISPR associated protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S5U
Type: protein
Length: 1,678 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein
UniProt: C7UDU4
Ligands: CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative uncharacterized protein	protein	212	44% helix, 17% strand	C7UDU4
B	Putative uncharacterized protein	protein	199	44% helix, 19% strand	C7UDU4
C	Putative uncharacterized protein	protein	210	44% helix, 18% strand	C7UDU4
D	Putative uncharacterized protein	protein	212	43% helix, 19% strand	C7UDU4
E	Putative uncharacterized protein	protein	213	42% helix, 18% strand	C7UDU4
F	Putative uncharacterized protein	protein	210	42% helix, 20% strand	C7UDU4
G	Putative uncharacterized protein	protein	209	44% helix, 18% strand	C7UDU4
H	Putative uncharacterized protein	protein	213	43% helix, 19% strand	C7UDU4

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, G, B, D, C, E, F, H

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.79	0.81	79	empty
2	914	0.74	0.78	67	empty
3	427	0.69	0.81	44	empty
4	197	0.59	0.81	34	empty
5	191	0.59	0.81	30	empty

Interfaces

13 interfaces between chains.

F–H · 2185 Å² buried · 32 hydrogen bonds · protein-protein
C–E · 2175 Å² buried · 33 hydrogen bonds · protein-protein
A–G · 2173 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 2122 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 1082 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3S5U · Crystal structure of CRISPR associated protein · the same entry in another collection · chain H against H, TM-score 1.00
C7UDU4 · AlphaFold monomer V2.0 prediction for CRISPR-associated protein CSN2 (C7UDU4) · a predicted model of the same protein · chain F 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 C7UDU4
Elsewhere: RCSB PDB 3S5U · PDBe 3S5U · UniProt C7UDU4

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