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Cryo-EM structure of deptor bound to human mtor complex 2, dept-bound subset local refinement

Analyse Cryo-EM structure of deptor bound to human mtor complex 2, dept-bound subset… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PE9
Type: protein
Length: 4,043 residues
Chains: 5
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, Q8TB45
Ligands: IHP, ACE, ZN
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 57% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1)	protein	2194	67% helix, 2% strand	P42345
C	Target of rapamycin complex subunit LST8	protein	319	0% helix, 47% strand	Q9BVC4
E	Rapamycin-insensitive companion of mtor	protein	1115	60% helix, 1% strand	Q6R327
G	Target of rapamycin complex 2 subunit MAPKAP1	protein	98	41% helix, 3% strand	Q9BPZ7
I	Dep domain-containing mtor-interacting protein	protein	317	38% helix, 21% strand	Q8TB45

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A
ACE · Acetyl group · ligand · chains E, G
ZN · Zinc ion · metal · chains E

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

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	1052	0.82	0.83	83	empty
2	1006	0.79	0.81	68	empty
3	605	0.77	0.83	75	empty
4	500	0.76	0.84	67	empty
5	1036	0.75	0.78	80	empty

Interfaces

5 interfaces between chains.

A–E · 3576 Å² buried · 18 hydrogen bonds · protein-protein
E–G · 2277 Å² buried · 17 hydrogen bonds · protein-protein
A–I · 2069 Å² buried · 18 hydrogen bonds · protein-protein
C–G · 1347 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 885 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7PE9 · cryo-EM structure of DEPTOR bound to human mTOR complex 2, DEPt-bound subset local… · the same entry in another collection · chain I against I, 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 0.96
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 0.95
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 0.87
Q8TB45 · AlphaFold monomer V2.0 prediction for dep domain-containing mtor- interacting protein… · a predicted model of the same protein · chain I against A, TM-score 0.62
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 0.37

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
Every structure of UniProt Q8TB45
Elsewhere: RCSB PDB 7PE9 · PDBe 7PE9 · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7 · UniProt Q8TB45

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