Research workbench

4.9 ångström cryo-EM structure of human mtor complex 2

Analyse 4.9 ångström cryo-EM structure of human mtor complex 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZCS
Type: protein
Length: 6,922 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase mtor; Target of rapamycin complex subunit LST8…
EC: 2.7.11.1
UniProt: P42345, Q9BVC4, Q6R327, Q9BPZ7
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 4 distinct chains · 46% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1)	protein	2178	48% helix, 1% strand	P42345
C, D	Target of rapamycin complex subunit LST8	protein	317	0% helix, 36% strand	Q9BVC4
E, F	Rapamycin-insensitive companion of mtor	protein	880	60% helix, 0% strand	Q6R327
G, H	Target of rapamycin complex 2 subunit MAPKAP1	protein	86	48% helix, 0% strand	Q9BPZ7

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.90	0.92	140	empty
2	740	0.89	0.92	92	empty
3	710	0.89	0.92	83	empty
4	1184	0.88	0.89	123	empty
5	545	0.86	0.92	76	empty

Interfaces

13 interfaces between chains.

A–B · 2192 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 874 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 821 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 628 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 588 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5ZCS · 4.9 Angstrom Cryo-EM structure of human mTOR complex 2 · the same entry in another collection · chain H against H, TM-score 1.00
Q9BVC4 · AlphaFold monomer V2.0 prediction for target of rapamycin complex subunit LST8 (Q9BVC4) · a predicted model of the same protein · chain C against A, TM-score 0.92
P42345 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase mtor (P42345) · a predicted model of the same protein · chain A against A, TM-score 0.85
Q6R327 · AlphaFold monomer V2.0 prediction for rapamycin-insensitive companion of mtor (Q6R327) · a predicted model of the same protein · chain E against A, TM-score 0.40
Q9BPZ7 · AlphaFold monomer V2.0 prediction for target of rapamycin complex 2 subunit MAPKAP1… · a predicted model of the same protein · chain G against A, TM-score 0.40

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 P42345
Every structure of UniProt Q9BVC4
Every structure of UniProt Q6R327
Every structure of UniProt Q9BPZ7
Elsewhere: RCSB PDB 5ZCS · PDBe 5ZCS · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7

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