SMTL ID : 7pe7.1

cryo-EM structure of DEPTOR bound to human mTOR complex 2, overall refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.41 Å

Oligo State

hetero-2-2-2-2-2-mer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 8 residues within 4Å: Chain A: K.1677, S.1680, K.1684, Y.1720, K.1724, R.1771, W.1808, K.1810 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.1650, A:S.1680, A:Y.1720 Salt bridges: A:K.1677, A:K.1677, A:K.1677, A:K.1684, A:K.1724, A:K.1724, A:K.1724, A:R.1771, A:K.1810, A:K.1810 IHP.4: 8 residues within 4Å: Chain E: K.1677, S.1680, K.1684, Y.1720, K.1724, R.1771, W.1808, K.1810 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.1650, E:S.1680 Salt bridges: E:K.1677, E:K.1677, E:K.1677, E:K.1684, E:K.1724, E:K.1724, E:K.1724, E:R.1771, E:K.1810, E:K.1810

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain C: H.1515, C.1520, C.1523, C.1651 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.1515, C:C.1520, C:C.1523, C:C.1651 ZN.5: 4 residues within 4Å: Chain G: H.1515, C.1520, C.1523, C.1651 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.1515, G:C.1520, G:C.1523, G:C.1651

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.3: 5 residues within 4Å: Chain C: R.293, W.295, Y.391, Y.970 Chain D: A.2 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.391 ACE.6: 5 residues within 4Å: Chain G: R.293, W.295, Y.391, Y.970 Chain H: A.2 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walchli, M. et al., Regulation of human mTOR complexes by DEPTOR. Elife (2021)

Release Date

2021-09-15

Peptides

Serine/threonine-protein kinase mTOR: AE
Target of rapamycin complex subunit LST8: BF
Rapamycin-insensitive companion of mTOR: CG
Target of rapamycin complex 2 subunit MAPKAP1: DH
DEP domain-containing mTOR-interacting protein: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
A

B
D

F
C

C
F

G
E

D
H

H
G

I
I

J
J

Serine/threonine-protein kinase mTOR

Target of rapamycin complex subunit LST8

Rapamycin-insensitive companion of mTOR

Target of rapamycin complex 2 subunit MAPKAP1

DEP domain-containing mTOR-interacting protein

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