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Crystal structure of CASTOR1-arginine

Analyse Crystal structure of CASTOR1-arginine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GS9
Type: protein
Length: 1,175 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gats-like protein 3
UniProt: Q8WTX7
Ligands: ARG
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gats-like protein 3	protein	309	29% helix, 31% strand	Q8WTX7
B	Gats-like protein 3	protein	286	31% helix, 34% strand	Q8WTX7
C	Gats-like protein 3	protein	294	28% helix, 32% strand	Q8WTX7
D	Gats-like protein 3	protein	286	28% helix, 34% strand	Q8WTX7

Ligands and binding sites

ARG · Arginine · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.79	0.80	103	empty
2	50	0.66	0.96	22	ARG
3	154	0.48	0.77	28	empty
4	222	0.46	0.74	27	empty
5	139	0.43	0.75	26	empty

Interfaces

5 interfaces between chains.

C–D · 992 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 943 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 758 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 90 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 50 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GS9 · Crystal structure of CASTOR1-arginine · the same entry in another collection · chain D against D, TM-score 1.00
Q8WTX7 · AlphaFold monomer V2.0 prediction for cytosolic arginine sensor for MTORC1 subunit 1… · a predicted model of the same protein · chain B 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 Q8WTX7
Elsewhere: RCSB PDB 5GS9 · PDBe 5GS9 · UniProt Q8WTX7

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