SMTL ID : 7t3b.1

GATOR1-RAG-RAGULATOR - GAP Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)(Covalent)

GDP.1: 18 residues within 4Å: Chain A: R.71, S.72, G.73, K.74, S.75, S.76, T.90, L.91, E.94, S.95, T.96, H.178, K.179, D.181, S.219, I.220, Y.221 Ligands: AF3.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.71, A:S.72, A:G.73, A:K.74, A:S.75, A:S.75, A:S.76, A:T.90, A:T.90, A:T.96, A:T.96, A:K.179, A:I.220, A:Y.221, A:Y.221 Salt bridges: A:R.71, A:K.74, A:D.181 pi-Cation interactions: A:K.179 GDP.3: 19 residues within 4Å: Chain B: R.78 Chain J: G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, G.40, A.41, T.42, H.127, K.128, D.130, S.163, I.164, W.165 Ligands: AF3.4 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain J Salt bridges: B:R.78, B:R.78, J:K.20, J:K.20, J:D.130 Hydrogen bonds: J:G.17, J:T.21, J:T.21, J:S.22, J:T.36, J:T.42, J:K.128, J:K.128, J:I.164 pi-Cation interactions: J:K.128

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2: 9 residues within 4Å: Chain A: R.70, R.71, K.74, S.95, T.96, N.97, F.117, G.119 Ligands: GDP.1 No protein-ligand interaction detected (PLIP) AF3.4: 10 residues within 4Å: Chain B: R.78 Chain J: K.15, S.16, G.17, K.20, T.42, C.63, G.65, Q.66 Ligands: GDP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egri, S.B. et al., Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. Mol.Cell (2022)

Release Date

2022-04-06

Peptides

Ras-related GTP-binding protein C: A
GATOR complex protein NPRL2: B
GATOR complex protein DEPDC5: C
Ragulator complex protein LAMTOR3: D
Ragulator complex protein LAMTOR2: E
Ragulator complex protein LAMTOR5: F
Ragulator complex protein LAMTOR4: G
Ragulator complex protein LAMTOR1: H
GATOR complex protein NPRL3: I
Ras-related GTP-binding protein A: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
B

C
A

D
H

E
G

F
J

G
I

H
F

I
C

J
D

Ras-related GTP-binding protein C

GATOR complex protein NPRL2

GATOR complex protein DEPDC5

Ragulator complex protein LAMTOR3

Ragulator complex protein LAMTOR2

Ragulator complex protein LAMTOR5

Ragulator complex protein LAMTOR4

Ragulator complex protein LAMTOR1

GATOR complex protein NPRL3

Ras-related GTP-binding protein A

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