SMTL ID : 6zwm.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 13 residues within 4Å: Chain A: S.2165, Q.2167, L.2185, K.2187, E.2190, I.2237, G.2238, W.2239, V.2240, T.2245, S.2342, M.2345, D.2357 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.2165, A:Q.2167, A:G.2238, A:V.2240, A:T.2245, A:T.2245, A:D.2357 Salt bridges: A:K.2187 pi-Stacking: A:W.2239 AGS.3: 13 residues within 4Å: Chain B: S.2165, Q.2167, L.2185, K.2187, E.2190, I.2237, G.2238, W.2239, V.2240, T.2245, S.2342, M.2345, D.2357 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.2165, B:Q.2167, B:Q.2167, B:G.2238, B:V.2240, B:T.2245, B:T.2245, B:D.2357 Salt bridges: B:K.2187 pi-Stacking: B:W.2239 AGS.6: 7 residues within 4Å: Chain E: K.541, N.543, R.572, R.575, R.576, Y.579, L.587 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.541, E:N.543, E:N.543 Salt bridges: E:R.572, E:R.575, E:R.576, E:R.576 AGS.8: 7 residues within 4Å: Chain F: K.541, N.543, R.572, R.575, R.576, Y.579, L.587 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:K.541, F:N.543, F:N.543 Salt bridges: F:K.541, F:R.572, F:R.575, F:R.576

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 8 residues within 4Å: Chain A: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.1658 Salt bridges: A:K.1655, A:K.1655, A:K.1655, A:K.1662, A:K.1662, A:K.1702, A:K.1702, A:K.1702, A:R.1749, A:K.1753 IHP.4: 8 residues within 4Å: Chain B: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.1658 Salt bridges: B:K.1655, B:K.1655, B:K.1655, B:K.1662, B:K.1662, B:K.1702, B:K.1702, B:K.1702, B:R.1749, B:K.1753, B:K.1753

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain E: H.1515, C.1520, C.1523, C.1651 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.1515, E:C.1520, E:C.1523, E:C.1651 ZN.7: 4 residues within 4Å: Chain F: H.1515, C.1520, C.1523, C.1651 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.1515, F:C.1520, F:C.1523, F:C.1651

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

ACE.9: 7 residues within 4Å: Chain E: R.293, W.295, Y.391, L.847, Y.970 Chain G: A.2, F.3 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.295, E:Y.391 Hydrogen bonds: E:Y.970 ACE.10: 8 residues within 4Å: Chain F: R.293, W.295, Y.391, L.847, L.851, Y.970 Chain H: A.2, F.3 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.391 Hydrogen bonds: F:Y.970

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scaiola, A. et al., The 3.2- angstrom resolution structure of human mTORC2. Sci Adv (2020)

Release Date

2020-11-18

Peptides

Serine/threonine-protein kinase mTOR: AB
Target of rapamycin complex subunit LST8: CD
Rapamycin-insensitive companion of mTOR: EF
Target of rapamycin complex 2 subunit MAPKAP1: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Serine/threonine-protein kinase mTOR

Target of rapamycin complex subunit LST8

Rapamycin-insensitive companion of mTOR

Target of rapamycin complex 2 subunit MAPKAP1

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