SMTL ID : 7tvf.2 (1 other biounit)

Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: C.126, S.128, I.129, V.194, P.195, D.196, W.205, V.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.128, A:S.128, A:P.195 GOL.6: 7 residues within 4Å: Chain A: Q.180, S.181 Chain B: S.50, Y.51, L.52, D.65 Chain C: K.109 7 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:S.50, B:S.50, B:S.50, C:K.109 Water bridges: A:Q.180, A:S.181, A:R.187 GOL.9: 6 residues within 4Å: Chain A: E.183, R.186 Chain C: N.156, H.178, N.179, K.180 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.156, C:N.179, A:R.186, A:R.186 GOL.10: 8 residues within 4Å: Chain C: F.375, S.376, A.378, K.379, T.400, W.401, T.402, S.403 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.379, C:K.379, C:W.401, C:T.402, C:S.403 GOL.11: 7 residues within 4Å: Chain A: E.43, S.47 Chain C: N.271, Y.293, N.294, R.295, N.316 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.294, C:N.316, C:N.316, A:E.43 GOL.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: Q.48, P.49, E.53, L.54, E.115, F.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.53, A:E.115 Water bridges: A:E.53 SO4.7: 4 residues within 4Å: Chain B: D.166, K.167, H.170, R.174 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.166 Water bridges: B:D.58, B:K.167, B:R.174 Salt bridges: B:H.170, B:R.174 SO4.13: 4 residues within 4Å: Chain C: K.416, P.418, E.419, D.420 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.419, C:D.420 Water bridges: C:E.419, C:E.419

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: D.63, D.91, N.123, H.172, H.247 Ligands: MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.91, A:H.172, A:H.247, H2O.3 MN.4: 4 residues within 4Å: Chain A: D.63, H.65, D.91 Ligands: MN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.63, A:H.65, A:D.91, H2O.3, H2O.5

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.5: 26 residues within 4Å: Chain B: D.22, G.23, G.24, V.25, G.26, K.27, S.28, A.29, F.39, V.40, P.41, D.42, Y.43, P.45, T.46, A.70, G.71, L.72, N.127, K.128, D.130, L.131, S.157, A.158, K.159 Ligands: MG.8 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:G.24, B:V.25, B:G.26, B:K.27, B:K.27, B:K.27, B:S.28, B:A.29, B:V.40, B:T.46, B:T.46, B:T.69, B:G.71, B:L.72, B:N.127, B:K.128, B:K.128, B:A.158, B:K.159 Water bridges: B:P.41, B:Y.43, B:D.44, B:K.159 Salt bridges: B:D.130 pi-Stacking: B:F.39, B:F.39 pi-Cation interactions: B:K.128

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain B: S.28, T.46, D.68 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.28, B:T.46, H2O.6, H2O.7

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 3 residues within 4Å: Chain A: E.53, E.55 Chain C: R.182 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: Q.353, F.354, S.355, T.356, I.357 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: H.236, K.237 Chain C: K.134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonsor, D.A. et al., Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-05-04

Peptides

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit: A
Ras-related protein M-Ras: B
Leucine-rich repeat protein SHOC-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Ras-related protein M-Ras

Leucine-rich repeat protein SHOC-2

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