MolNFT v1 · #121674 · protein

Arginine-bound CASTOR1 from homo sapiens

5I2C · Gats-like protein 3: “Arginine-bound CASTOR1 from homo sapiens”. X-ray diffraction, 1 ligand (ARG), 8 pockets (best druggability 0.79). MolNFT v1 #121674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I2C
Type: protein
Length: 1,156 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: 8 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gats-like protein 3	protein	301	30% helix, 32% strand	Q8WTX7
B	Gats-like protein 3	protein	283	32% helix, 34% strand	Q8WTX7
C	Gats-like protein 3	protein	285	32% helix, 33% strand	Q8WTX7
D	Gats-like protein 3	protein	287	31% helix, 32% strand	Q8WTX7

Ligands and binding sites

ARG · Arginine · ligand · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.79	0.80	121	empty
2	54	0.68	0.97	27	ARG
3	317	0.54	0.75	31	empty
4	105	0.42	0.77	26	empty
5	86	0.40	0.78	18	empty

Interfaces

5 interfaces between chains.

A–B · 964 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 942 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 800 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 159 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 59 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5I2C · Arginine-bound CASTOR1 from Homo sapiens · 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 0.98

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 Q8WTX7
Elsewhere: RCSB PDB 5I2C · PDBe 5I2C · UniProt Q8WTX7

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