SMTL ID : 9mhf.1

Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 19 residues within 4Å: Chain A: L.32, V.40, V.51, K.53, R.103, Y.105, V.106, R.107, D.108, N.109, D.148, K.150, E.152, N.153, M.155, D.166, K.171, T.189 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:V.106, A:V.106, A:V.106, A:D.148, A:N.153, A:T.189 Water bridges: A:K.53, A:N.109 Salt bridges: A:K.53, A:K.53, A:K.53, A:K.150, A:K.150, A:K.171 pi-Stacking: A:Y.105 pi-Cation interactions: A:Y.105 GTP.4: 24 residues within 4Å: Chain E: D.40, S.41, G.42, V.43, G.44, K.45, S.46, C.47, Y.57, E.59, S.60, Y.61, S.63, T.64, T.88, G.90, N.145, K.146, D.148, L.149, S.175, A.176, K.177 Ligands: MG.5 28 PLIP interactions: 28 interactions with chain E Hydrogen bonds: E:G.42, E:V.43, E:G.44, E:K.45, E:S.46, E:S.46, E:C.47, E:E.59, E:E.59, E:S.60, E:T.64, E:T.64, E:T.64, E:T.88, E:G.90, E:N.145, E:K.146, E:K.146, E:S.175, E:A.176, E:K.177 Water bridges: E:L.91, E:L.91 Salt bridges: E:K.45, E:K.45, E:D.148 pi-Stacking: E:Y.57, E:Y.57

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.53, N.153, D.166 Ligands: GTP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.166, H2O.1 MG.5: 4 residues within 4Å: Chain E: S.46, T.64, D.87 Ligands: GTP.4 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.46, E:T.64, E:D.87, H2O.1, H2O.1

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.3: 11 residues within 4Å: Chain A: F.37, F.38, F.55, L.62, L.64, Y.67, K.68, E.92, A.99, Y.185, F.186 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.38, A:F.55, A:L.62, A:L.64, A:Y.67, A:K.68, A:E.92, A:A.99, A:Y.185, A:F.186, A:F.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, A.S.I. et al., Structural pathway for class III PI 3-kinase activation by the myristoylated GTPbindingpseudokinase VPS15. To Be Published

Release Date

2025-02-12

Peptides

Phosphoinositide 3-kinase regulatory subunit 4: A
Phosphatidylinositol 3-kinase catalytic subunit type 3: B
Beclin 1-associated autophagy-related key regulator: C
Beclin-1: D
Ras-related protein Rab-1A: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Phosphoinositide 3-kinase regulatory subunit 4

Phosphatidylinositol 3-kinase catalytic subunit type 3

Beclin 1-associated autophagy-related key regulator

Beclin-1

Ras-related protein Rab-1A

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