SMTL ID : 9mhh.1

PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation

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: 9 residues within 4Å: Chain A: L.32, V.106, R.107, D.108, N.109, D.148, E.152, N.153 Ligands: MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.106, A:R.107, A:R.107, A:N.109, A:E.152 GTP.4: 19 residues within 4Å: Chain E: D.40, G.42, V.43, G.44, K.45, S.46, C.47, T.58, E.59, S.60, Y.61, S.63, T.64, G.90, K.146, S.175, A.176, K.177 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.42, E:V.43, E:G.44, E:K.45, E:C.47, E:E.59, E:S.60, E:T.64, E:G.90, E:K.146, E:A.176, E:K.177

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain E: G.44, K.45, S.46, C.47 Ligands: GTP.4 No protein-ligand interaction detected (PLIP)

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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