SMTL ID : 2mse.1

NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc

Coordinates

PDB Format Compare

Method

SOLUTION NMR

Oligo State

hetero-2-1-1-mer

Ligands

64 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-functional Binders)(Non-covalent)

PCW.1: 6 residues within 4Å: Ligands: PCW.26, PCW.28, PCW.32, 17F.35, 17F.38, PCW.68 Ligand excluded by PLIP PCW.2: 9 residues within 4Å: Chain A: Y.151, A.155, H.158 Chain B: F.30 Ligands: PCW.5, PCW.17, PCW.21, PCW.53, PCW.56 Ligand excluded by PLIP PCW.3: 7 residues within 4Å: Chain A: L.85, A.89, K.92 Chain C: Q.45 Ligands: PCW.13, PCW.18, PCW.19 Ligand excluded by PLIP PCW.4: 5 residues within 4Å: Chain A: Y.195 Ligands: PCW.7, PCW.16, PCW.32, PCW.61 Ligand excluded by PLIP PCW.5: 5 residues within 4Å: Ligands: PCW.2, PCW.17, 17F.36, 17F.38, 17F.40 Ligand excluded by PLIP PCW.6: 7 residues within 4Å: Ligands: PCW.7, PCW.11, PCW.16, PCW.20, PCW.24, PCW.28, 17F.39 Ligand excluded by PLIP PCW.7: 4 residues within 4Å: Ligands: PCW.4, PCW.6, PCW.16, 17F.33 Ligand excluded by PLIP PCW.8: 5 residues within 4Å: Ligands: PCW.10, PCW.22, PCW.27, 17F.37, 17F.73 Ligand excluded by PLIP PCW.9: 9 residues within 4Å: Chain D: Y.6 Ligands: PCW.11, PCW.14, PCW.26, PCW.28, PCW.29, PCW.30, 17F.34, PCW.69 Ligand excluded by PLIP PCW.10: 5 residues within 4Å: Ligands: PCW.8, PCW.12, PCW.21, PCW.22, 17F.36 Ligand excluded by PLIP PCW.11: 9 residues within 4Å: Ligands: PCW.6, PCW.9, PCW.24, PCW.25, PCW.28, 17F.39, PCW.60, PCW.63, 17F.75 Ligand excluded by PLIP PCW.12: 13 residues within 4Å: Chain D: I.47, K.48, R.50, K.51, T.52 Ligands: PCW.10, PCW.17, PCW.22, PCW.30, 17F.36, 17F.40, PCW.43, PCW.70 Ligand excluded by PLIP PCW.13: 9 residues within 4Å: Ligands: PCW.3, PCW.14, PCW.18, PCW.23, PCW.27, 17F.34, 17F.37, PCW.49, 17F.80 Ligand excluded by PLIP PCW.14: 8 residues within 4Å: Chain D: Y.6, K.10 Ligands: PCW.9, PCW.13, PCW.23, PCW.30, 17F.34, 17F.37 Ligand excluded by PLIP PCW.15: 6 residues within 4Å: Chain A: F.16 Chain C: K.186 Ligands: PCW.16, PCW.20, PCW.24, 17F.39 Ligand excluded by PLIP PCW.16: 8 residues within 4Å: Chain C: K.186 Ligands: PCW.4, PCW.6, PCW.7, PCW.15, PCW.20, PCW.24, 17F.39 Ligand excluded by PLIP PCW.17: 7 residues within 4Å: Ligands: PCW.2, PCW.5, PCW.12, PCW.21, 17F.36, 17F.38, PCW.51 Ligand excluded by PLIP PCW.18: 10 residues within 4Å: Chain D: E.71, V.72 Ligands: PCW.3, PCW.13, PCW.19, PCW.23, PCW.27, 17F.37, PCW.49, PCW.65 Ligand excluded by PLIP PCW.19: 7 residues within 4Å: Chain C: M.3, E.5 Ligands: PCW.3, PCW.18, PCW.23, PCW.25, PCW.29 Ligand excluded by PLIP PCW.20: 15 residues within 4Å: Chain A: L.41, M.45 Chain B: R.136 Chain C: K.106, S.108, K.177, K.178, S.183, C.187 Ligands: PCW.6, PCW.15, PCW.16, PCW.25, PCW.31, PCW.72 Ligand excluded by PLIP PCW.21: 7 residues within 4Å: Chain A: Y.151 Ligands: PCW.2, PCW.10, PCW.17, PCW.22, 17F.36, PCW.51 Ligand excluded by PLIP PCW.22: 5 residues within 4Å: Chain D: R.50 Ligands: PCW.8, PCW.10, PCW.12, PCW.21 Ligand excluded by PLIP PCW.23: 10 residues within 4Å: Chain D: P.8, K.10, E.71 Ligands: PCW.13, PCW.14, PCW.18, PCW.19, 17F.34, 17F.37, PCW.49 Ligand excluded by PLIP PCW.24: 12 residues within 4Å: Chain C: V.105, K.106, D.107, C.187 Ligands: PCW.6, PCW.11, PCW.15, PCW.16, PCW.25, 17F.39, PCW.60, PCW.63 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Chain C: E.5, K.7, E.78 Ligands: PCW.11, PCW.19, PCW.20, PCW.24, PCW.29, PCW.31 Ligand excluded by PLIP PCW.26: 5 residues within 4Å: Ligands: PCW.1, PCW.9, PCW.28, 17F.40, PCW.69 Ligand excluded by PLIP PCW.27: 8 residues within 4Å: Chain D: Y.44, E.71, L.73 Ligands: PCW.8, PCW.13, PCW.18, 17F.37, 17F.76 Ligand excluded by PLIP PCW.28: 6 residues within 4Å: Ligands: PCW.1, PCW.6, PCW.9, PCW.11, PCW.26, PCW.63 Ligand excluded by PLIP PCW.29: 9 residues within 4Å: Chain B: Y.125 Chain C: T.4, Y.6, E.51 Ligands: PCW.9, PCW.19, PCW.25, PCW.31, PCW.50 Ligand excluded by PLIP PCW.30: 13 residues within 4Å: Chain D: L.46, K.48, G.49, R.50, K.51, I.69 Ligands: PCW.9, PCW.12, PCW.14, 17F.34, 17F.37, 17F.40, PCW.43 Ligand excluded by PLIP PCW.31: 7 residues within 4Å: Chain C: K.169, M.172, K.177, K.178 Ligands: PCW.20, PCW.25, PCW.29 Ligand excluded by PLIP PCW.32: 6 residues within 4Å: Chain A: Y.195 Ligands: PCW.1, PCW.4, 17F.33, 17F.35, 17F.38 Ligand excluded by PLIP PCW.41: 6 residues within 4Å: Ligands: PCW.42, PCW.52, PCW.58, PCW.59, PCW.60, PCW.61 Ligand excluded by PLIP PCW.42: 5 residues within 4Å: Ligands: PCW.41, PCW.52, PCW.63, PCW.69, 17F.75 Ligand excluded by PLIP PCW.43: 7 residues within 4Å: Ligands: PCW.12, PCW.30, 17F.40, PCW.68, PCW.69, PCW.70, 17F.75 Ligand excluded by PLIP PCW.44: 6 residues within 4Å: Ligands: 17F.35, PCW.53, PCW.55, PCW.59, PCW.64, 17F.77 Ligand excluded by PLIP PCW.45: 7 residues within 4Å: Ligands: PCW.47, PCW.49, PCW.57, PCW.71, 17F.74, 17F.75, 17F.79 Ligand excluded by PLIP PCW.46: 2 residues within 4Å: Ligands: PCW.71, 17F.73 Ligand excluded by PLIP PCW.47: 4 residues within 4Å: Ligands: PCW.45, PCW.71, 17F.73, 17F.76 Ligand excluded by PLIP PCW.48: 3 residues within 4Å: Ligands: PCW.54, PCW.58, PCW.60 Ligand excluded by PLIP PCW.49: 8 residues within 4Å: Ligands: PCW.13, PCW.18, PCW.23, PCW.45, PCW.57, PCW.65, 17F.79, 17F.80 Ligand excluded by PLIP PCW.50: 2 residues within 4Å: Ligands: PCW.29, 17F.78 Ligand excluded by PLIP PCW.51: 6 residues within 4Å: Ligands: PCW.17, PCW.21, 17F.36, PCW.56, PCW.70, PCW.71 Ligand excluded by PLIP PCW.52: 7 residues within 4Å: Ligands: 17F.33, PCW.41, PCW.42, PCW.58, PCW.60, PCW.62, PCW.63 Ligand excluded by PLIP PCW.53: 5 residues within 4Å: Ligands: PCW.2, PCW.44, PCW.55, PCW.56, PCW.64 Ligand excluded by PLIP PCW.54: 4 residues within 4Å: Ligands: PCW.48, PCW.60, PCW.62, PCW.72 Ligand excluded by PLIP PCW.55: 6 residues within 4Å: Chain B: W.9 Ligands: 17F.38, PCW.44, PCW.53, PCW.64, 17F.77 Ligand excluded by PLIP PCW.56: 6 residues within 4Å: Ligands: PCW.2, PCW.51, PCW.53, PCW.64, PCW.68, PCW.70 Ligand excluded by PLIP PCW.57: 4 residues within 4Å: Ligands: PCW.45, PCW.49, 17F.79, 17F.80 Ligand excluded by PLIP PCW.58: 5 residues within 4Å: Ligands: PCW.41, PCW.48, PCW.52, PCW.60, PCW.61 Ligand excluded by PLIP PCW.59: 4 residues within 4Å: Ligands: PCW.41, PCW.44, PCW.61, 17F.77 Ligand excluded by PLIP PCW.60: 9 residues within 4Å: Ligands: PCW.11, PCW.24, PCW.41, PCW.48, PCW.52, PCW.54, PCW.58, PCW.62, PCW.63 Ligand excluded by PLIP PCW.61: 4 residues within 4Å: Ligands: PCW.4, PCW.41, PCW.58, PCW.59 Ligand excluded by PLIP PCW.62: 7 residues within 4Å: Ligands: PCW.52, PCW.54, PCW.60, PCW.63, PCW.67, PCW.72, 17F.78 Ligand excluded by PLIP PCW.63: 10 residues within 4Å: Ligands: PCW.11, PCW.24, PCW.28, PCW.42, PCW.52, PCW.60, PCW.62, PCW.67, PCW.72, 17F.75 Ligand excluded by PLIP PCW.64: 5 residues within 4Å: Ligands: 17F.38, PCW.44, PCW.53, PCW.55, PCW.56 Ligand excluded by PLIP PCW.65: 3 residues within 4Å: Ligands: PCW.18, PCW.49, 17F.80 Ligand excluded by PLIP PCW.66: 3 residues within 4Å: Ligands: PCW.67, 17F.78, 17F.79 Ligand excluded by PLIP PCW.67: 8 residues within 4Å: Ligands: 17F.34, PCW.62, PCW.63, PCW.66, PCW.72, 17F.74, 17F.75, 17F.78 Ligand excluded by PLIP PCW.68: 6 residues within 4Å: Ligands: PCW.1, 17F.36, PCW.43, PCW.56, PCW.69, PCW.70 Ligand excluded by PLIP PCW.69: 6 residues within 4Å: Ligands: PCW.9, PCW.26, 17F.35, PCW.42, PCW.43, PCW.68 Ligand excluded by PLIP PCW.70: 7 residues within 4Å: Ligands: PCW.12, 17F.36, PCW.43, PCW.51, PCW.56, PCW.68, PCW.71 Ligand excluded by PLIP PCW.71: 6 residues within 4Å: Ligands: PCW.45, PCW.46, PCW.47, PCW.51, PCW.70, 17F.73 Ligand excluded by PLIP PCW.72: 6 residues within 4Å: Ligands: PCW.20, PCW.54, PCW.62, PCW.63, PCW.67, 17F.78 Ligand excluded by PLIP

16 x 17F: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine(Non-functional Binders)(Non-covalent)

17F.33: 4 residues within 4Å: Ligands: PCW.7, PCW.32, 17F.35, PCW.52 No protein-ligand interaction detected (PLIP) 17F.34: 8 residues within 4Å: Chain D: K.51, I.69 Ligands: PCW.9, PCW.13, PCW.14, PCW.23, PCW.30, PCW.67 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.51 17F.35: 6 residues within 4Å: Ligands: PCW.1, PCW.32, 17F.33, 17F.38, PCW.44, PCW.69 No protein-ligand interaction detected (PLIP) 17F.36: 10 residues within 4Å: Chain D: K.48 Ligands: PCW.5, PCW.10, PCW.12, PCW.17, PCW.21, 17F.40, PCW.51, PCW.68, PCW.70 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.48 Salt bridges: D:K.48, D:K.48 17F.37: 10 residues within 4Å: Chain D: Y.44, R.50, K.51 Ligands: PCW.8, PCW.13, PCW.14, PCW.18, PCW.23, PCW.27, PCW.30 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.44, D:R.50, D:R.50, D:K.51 Salt bridges: D:R.50, D:K.51 17F.38: 7 residues within 4Å: Ligands: PCW.1, PCW.5, PCW.17, PCW.32, 17F.35, PCW.55, PCW.64 No protein-ligand interaction detected (PLIP) 17F.39: 5 residues within 4Å: Ligands: PCW.6, PCW.11, PCW.15, PCW.16, PCW.24 No protein-ligand interaction detected (PLIP) 17F.40: 10 residues within 4Å: Chain D: L.46, I.47, K.48, G.49 Ligands: PCW.5, PCW.12, PCW.26, PCW.30, 17F.36, PCW.43 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.48, D:G.49 Salt bridges: D:K.48 17F.73: 5 residues within 4Å: Ligands: PCW.8, PCW.46, PCW.47, PCW.71, 17F.76 No protein-ligand interaction detected (PLIP) 17F.74: 4 residues within 4Å: Ligands: PCW.45, PCW.67, 17F.75, 17F.79 No protein-ligand interaction detected (PLIP) 17F.75: 7 residues within 4Å: Ligands: PCW.11, PCW.42, PCW.43, PCW.45, PCW.63, PCW.67, 17F.74 No protein-ligand interaction detected (PLIP) 17F.76: 4 residues within 4Å: Chain B: V.78 Ligands: PCW.27, PCW.47, 17F.73 No protein-ligand interaction detected (PLIP) 17F.77: 7 residues within 4Å: Chain B: L.3, L.192, Y.195, T.196 Ligands: PCW.44, PCW.55, PCW.59 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.3, B:Y.195 17F.78: 5 residues within 4Å: Ligands: PCW.50, PCW.62, PCW.66, PCW.67, PCW.72 No protein-ligand interaction detected (PLIP) 17F.79: 5 residues within 4Å: Ligands: PCW.45, PCW.49, PCW.57, PCW.66, 17F.74 No protein-ligand interaction detected (PLIP) 17F.80: 4 residues within 4Å: Ligands: PCW.13, PCW.49, PCW.57, PCW.65 No protein-ligand interaction detected (PLIP)

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

GNP.81: 19 residues within 4Å: Chain C: G.14, G.15, V.16, G.17, K.18, S.19, A.20, F.30, V.31, D.32, E.33, Y.34, D.35, P.36, T.37, N.118, K.119, A.148, K.149 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.15, C:G.17, C:K.18, C:S.19, C:S.19, C:S.19, C:A.20, C:V.31, C:E.33, C:Y.34, C:D.35, C:T.37, C:T.37, C:N.118, C:A.148, C:K.149 pi-Stacking: C:F.30, C:F.30 pi-Cation interactions: C:K.119, C:K.119

1 x MG: MAGNESIUM ION(Non-covalent)

MG.82: 4 residues within 4Å: Chain C: D.35, T.37, D.40, D.59 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.37, C:D.40, C:D.40, C:D.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazhab-Jafari, M.T. et al., Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-06-03

Peptides

Apolipoprotein A-I: AB
GTPase KRas: C
Serine/threonine-protein kinase A-Raf: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Apolipoprotein A-I

GTPase KRas

Serine/threonine-protein kinase A-Raf

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