SMTL ID : 5v7p.1

Atomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: N.183, F.184, N.185, L.187, V.188, Q.189, H.196, V.197, L.198, V.199, Y.204, H.209, P.210, S.211, Y.212, E.250, L.254, Y.265 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.187, A:Q.189, A:V.199, A:V.199, A:Y.204, A:H.209, A:S.211, A:Y.212, A:Y.212 Water bridges: A:Q.189

3 x UND: UNDECANE(Non-covalent)

UND.2: 1 residues within 4Å: Chain A: I.112 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.112 UND.3: 8 residues within 4Å: Chain A: F.21, C.24, M.25, H.28, L.79, Y.80, L.83, V.84 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:L.79, A:Y.80, A:L.83, A:V.84 UND.9: 3 residues within 4Å: Chain A: S.137, I.144, L.230 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.144, A:I.144, A:L.230

11 x D10: DECANE(Non-covalent)

D10.4: 2 residues within 4Å: Chain A: Y.217, P.274 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.274 D10.5: 9 residues within 4Å: Chain A: F.207, Y.217, G.270, T.271, G.272, I.273, P.274, I.276, E.277 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.207, A:Y.217, A:T.271 D10.6: 2 residues within 4Å: Chain A: L.178 Ligands: MPG.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.178 D10.7: 3 residues within 4Å: Chain A: W.139, V.140, F.143 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.139, A:F.143 D10.8: 6 residues within 4Å: Chain A: F.70, L.71, F.92, M.99, W.139 Ligands: D10.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.70, A:L.71, A:M.99, A:W.139 D10.10: 7 residues within 4Å: Chain A: L.35, I.81, P.86, I.89 Ligands: D10.8, D10.11, MPG.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.35, A:I.89 D10.11: 3 residues within 4Å: Chain A: I.89, F.143 Ligands: D10.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.89, A:F.143 D10.12: 1 residues within 4Å: Chain A: W.157 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.157, A:W.157 D10.13: 2 residues within 4Å: Chain A: F.148, F.149 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.148, A:F.148, A:F.148, A:F.149, A:F.149 D10.14: 3 residues within 4Å: Chain A: F.70, Y.131, W.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.70, A:Y.131, A:W.139 D10.15: 1 residues within 4Å: Chain A: H.127 No protein-ligand interaction detected (PLIP)

10 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)(Non-functional Binders)

MPG.16: 5 residues within 4Å: Chain A: V.171, L.172, V.203, W.206 Ligands: MPG.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.171, A:L.172, A:V.203 Water bridges: A:G.202 MPG.17: 6 residues within 4Å: Chain A: K.82, L.83, Q.90, I.91, H.156, N.160 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.82, A:K.82, A:L.83 Hydrogen bonds: A:N.160, A:N.160 Water bridges: A:K.82 Salt bridges: A:H.156 MPG.18: 7 residues within 4Å: Chain A: P.4, K.7, I.8, Q.11, G.15, F.56, Y.57 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.56 Hydrogen bonds: A:K.7 Salt bridges: A:K.7 MPG.19: 2 residues within 4Å: Ligands: D10.6, MPG.21 No protein-ligand interaction detected (PLIP) MPG.20: 4 residues within 4Å: Chain A: F.216, I.220, T.236, W.240 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.216, A:I.220, A:T.236, A:W.240, A:W.240 MPG.21: 6 residues within 4Å: Chain A: T.175, L.178, T.179, H.201 Ligands: MPG.19, MPG.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.175, A:L.178 Hydrogen bonds: A:H.201 MPG.22: 2 residues within 4Å: Ligands: MPG.16, MPG.21 No protein-ligand interaction detected (PLIP) MPG.23: 7 residues within 4Å: Chain A: T.33, L.35, N.38, T.39, Y.80, V.84 Ligands: D10.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.33 MPG.24: 8 residues within 4Å: Chain A: L.18, V.19, V.22, I.23, F.26, N.27, I.41, Y.45 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.18, A:V.19, A:V.22, A:V.22, A:I.23 Hydrogen bonds: A:N.27 MPG.25: 17 residues within 4Å: Chain A: Y.95, M.99, V.124, I.125, N.126, Y.131, A.134, S.138, W.215, W.218, S.219, T.222, Q.223, Y.235, S.239 Chain B: S.78, W.81 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.124, A:Y.131, A:A.134, A:W.215, A:Y.235, A:Y.235, B:W.81 Hydrogen bonds: A:S.138, A:S.138, A:Q.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diver, M.M. et al., Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature (2018)

Release Date

2018-01-17

Peptides

Protein-S-isoprenylcysteine O-methyltransferase: A
monobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Membrane

We predict this structure to be a membrane protein.
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Protein-S-isoprenylcysteine O-methyltransferase

monobody