MolNFT v1 · #189557 · protein

Crystal structure of D. melanogaster samtor in the sah bound form

7VKQ · S-adenosylmethionine sensor upstream of MTORC1: “Crystal structure of D. melanogaster samtor in the sah bound form”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.78). MolNFT v1 #189557 on GenesisL1: 3D…

PDB: 7VKQ
Type: protein
Length: 873 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-adenosylmethionine sensor upstream of MTORC1
EC: 2.1.1.-
UniProt: Q9W138
Ligands: SAH
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-)	protein	228	33% helix, 28% strand	Q9W138
B	S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-)	protein	225	34% helix, 28% strand	Q9W138
C	S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-)	protein	210	35% helix, 30% strand	Q9W138
D	S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-)	protein	210	35% helix, 30% strand	Q9W138

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.78	0.80	66	empty
2	751	0.76	0.81	58	empty
3	414	0.66	0.79	45	empty
4	311	0.60	0.78	39	empty
5	361	0.58	0.76	33	empty

Interfaces

4 interfaces between chains.

A–C · 829 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 387 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 376 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 139 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7VKQ · Crystal structure of D. melanogaster SAMTOR in the SAH bound form · the same entry in another collection · chain D against D, TM-score 1.00
Q9W138 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine sensor upstream of MTORC1… · 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 Q9W138
Elsewhere: RCSB PDB 7VKQ · PDBe 7VKQ · UniProt Q9W138

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