SMTL ID : 2msc.1

NMR data-driven model of GTPase KRas-GDP tethered to a lipid-bilayer nanodisc

Coordinates

PDB Format Compare

Method

SOLUTION NMR

Oligo State

hetero-2-1-mer

Ligands

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

PCW.1: 7 residues within 4Å: Ligands: PCW.12, PCW.17, PCW.26, 17F.35, 17F.36, 17F.38, 17F.40 Ligand excluded by PLIP PCW.2: 5 residues within 4Å: Chain A: H.158 Ligands: PCW.5, PCW.17, PCW.53, PCW.56 Ligand excluded by PLIP PCW.3: 4 residues within 4Å: Ligands: PCW.13, PCW.18, PCW.19, PCW.23 Ligand excluded by PLIP PCW.4: 10 residues within 4Å: Chain C: R.125, T.129, E.145, Q.152 Ligands: PCW.7, PCW.16, PCW.32, 17F.33, 17F.39, PCW.58 Ligand excluded by PLIP PCW.5: 6 residues within 4Å: Ligands: PCW.2, PCW.17, 17F.36, 17F.38, PCW.53, PCW.64 Ligand excluded by PLIP PCW.6: 9 residues within 4Å: Chain C: D.156, Y.159 Ligands: PCW.11, PCW.16, PCW.24, PCW.28, 17F.39, PCW.60, PCW.63 Ligand excluded by PLIP PCW.7: 7 residues within 4Å: Chain C: T.129, Q.133, E.145 Ligands: PCW.4, PCW.16, 17F.33, 17F.35 Ligand excluded by PLIP PCW.8: 10 residues within 4Å: Chain A: L.122 Chain B: Y.59, F.63, W.67 Chain C: K.184, T.185 Ligands: PCW.10, PCW.22, PCW.27, 17F.73 Ligand excluded by PLIP PCW.9: 9 residues within 4Å: Chain C: D.49, G.50 Ligands: PCW.11, PCW.14, PCW.25, PCW.26, PCW.28, PCW.30, 17F.34 Ligand excluded by PLIP PCW.10: 8 residues within 4Å: Chain C: K.181, K.184, K.186 Ligands: PCW.8, PCW.12, PCW.21, PCW.22, 17F.36 Ligand excluded by PLIP PCW.11: 11 residues within 4Å: Chain C: V.47, D.49, R.163 Ligands: PCW.6, PCW.9, PCW.16, PCW.24, PCW.26, PCW.28, PCW.60, PCW.63 Ligand excluded by PLIP PCW.12: 14 residues within 4Å: Chain C: S.173, K.174, D.175, G.176, K.186, C.187 Ligands: PCW.1, PCW.10, PCW.22, PCW.30, 17F.36, 17F.40, PCW.43, PCW.51 Ligand excluded by PLIP PCW.13: 8 residues within 4Å: Ligands: PCW.3, PCW.14, PCW.18, PCW.19, PCW.23, PCW.30, 17F.34, 17F.37 Ligand excluded by PLIP PCW.14: 7 residues within 4Å: Ligands: PCW.9, PCW.13, PCW.22, PCW.23, PCW.30, 17F.34, 17F.37 Ligand excluded by PLIP PCW.15: 8 residues within 4Å: Chain A: F.16, L.19, R.20, W.31 Chain C: T.150, R.151 Ligands: PCW.16, 17F.39 Ligand excluded by PLIP PCW.16: 11 residues within 4Å: Chain C: Q.152, G.153 Ligands: PCW.4, PCW.6, PCW.7, PCW.11, PCW.15, PCW.24, PCW.28, 17F.39, PCW.60 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Ligands: PCW.1, PCW.2, PCW.5, PCW.21, 17F.36 Ligand excluded by PLIP PCW.18: 4 residues within 4Å: Ligands: PCW.3, PCW.13, PCW.23, 17F.37 Ligand excluded by PLIP PCW.19: 4 residues within 4Å: Ligands: PCW.3, PCW.13, PCW.23, PCW.29 Ligand excluded by PLIP PCW.20: 4 residues within 4Å: Chain A: L.41 Ligands: PCW.24, PCW.31, 17F.39 Ligand excluded by PLIP PCW.21: 8 residues within 4Å: Chain C: K.178, K.179, K.186 Ligands: PCW.10, PCW.17, PCW.22, 17F.36, PCW.51 Ligand excluded by PLIP PCW.22: 12 residues within 4Å: Chain C: T.185, K.186, C.187 Ligands: PCW.8, PCW.10, PCW.12, PCW.14, PCW.21, PCW.27, 17F.37, PCW.46, PCW.47 Ligand excluded by PLIP PCW.23: 7 residues within 4Å: Ligands: PCW.3, PCW.13, PCW.14, PCW.18, PCW.19, PCW.29, 17F.79 Ligand excluded by PLIP PCW.24: 11 residues within 4Å: Chain C: R.151, D.155, Y.159 Ligands: PCW.6, PCW.11, PCW.16, PCW.20, PCW.25, 17F.39, PCW.60, PCW.62 Ligand excluded by PLIP PCW.25: 7 residues within 4Å: Chain C: V.47, T.52 Ligands: PCW.9, PCW.24, PCW.29, PCW.31, PCW.67 Ligand excluded by PLIP PCW.26: 10 residues within 4Å: Chain C: D.49, R.163, K.167 Ligands: PCW.1, PCW.9, PCW.11, PCW.28, 17F.40, PCW.67, PCW.69 Ligand excluded by PLIP PCW.27: 5 residues within 4Å: Chain B: Y.74 Ligands: PCW.8, PCW.22, 17F.37, 17F.76 Ligand excluded by PLIP PCW.28: 12 residues within 4Å: Chain C: D.156, R.163 Ligands: PCW.6, PCW.9, PCW.11, PCW.16, PCW.26, 17F.39, PCW.42, PCW.52, PCW.63, PCW.67 Ligand excluded by PLIP PCW.29: 8 residues within 4Å: Chain A: D.48, V.52 Chain B: L.129 Ligands: PCW.19, PCW.23, PCW.25, PCW.31, PCW.67 Ligand excluded by PLIP PCW.30: 8 residues within 4Å: Chain C: E.170, S.173 Ligands: PCW.9, PCW.12, PCW.13, PCW.14, 17F.34, 17F.40 Ligand excluded by PLIP PCW.31: 4 residues within 4Å: Chain C: V.47 Ligands: PCW.20, PCW.25, PCW.29 Ligand excluded by PLIP PCW.32: 3 residues within 4Å: Ligands: PCW.4, 17F.33, 17F.35 Ligand excluded by PLIP PCW.41: 7 residues within 4Å: Ligands: PCW.42, PCW.48, PCW.52, PCW.58, PCW.59, PCW.61, 17F.77 Ligand excluded by PLIP PCW.42: 7 residues within 4Å: Ligands: PCW.28, 17F.39, PCW.41, PCW.52, PCW.63, PCW.69, 17F.75 Ligand excluded by PLIP PCW.43: 5 residues within 4Å: Ligands: PCW.12, PCW.68, PCW.69, PCW.70, 17F.75 Ligand excluded by PLIP PCW.44: 8 residues within 4Å: Ligands: 17F.33, PCW.53, PCW.55, PCW.59, PCW.64, PCW.68, PCW.69, 17F.77 Ligand excluded by PLIP PCW.45: 3 residues within 4Å: Ligands: PCW.49, 17F.74, 17F.79 Ligand excluded by PLIP PCW.46: 5 residues within 4Å: Chain B: V.52 Ligands: PCW.22, PCW.47, PCW.70, PCW.71 Ligand excluded by PLIP PCW.47: 6 residues within 4Å: Ligands: PCW.22, PCW.46, PCW.49, PCW.71, 17F.73, 17F.76 Ligand excluded by PLIP PCW.48: 5 residues within 4Å: Ligands: PCW.41, PCW.54, PCW.58, PCW.60, PCW.61 Ligand excluded by PLIP PCW.49: 8 residues within 4Å: Ligands: 17F.37, PCW.45, PCW.47, PCW.57, PCW.65, 17F.73, 17F.76, 17F.80 Ligand excluded by PLIP PCW.50: 1 residues within 4Å: Ligands: 17F.78 Ligand excluded by PLIP PCW.51: 5 residues within 4Å: Ligands: PCW.12, PCW.21, PCW.56, PCW.70, PCW.71 Ligand excluded by PLIP PCW.52: 4 residues within 4Å: Ligands: PCW.28, PCW.41, PCW.42, PCW.60 Ligand excluded by PLIP PCW.53: 8 residues within 4Å: Ligands: PCW.2, PCW.5, 17F.38, PCW.44, PCW.56, PCW.64, PCW.68, PCW.70 Ligand excluded by PLIP PCW.54: 3 residues within 4Å: Ligands: PCW.48, PCW.62, PCW.72 Ligand excluded by PLIP PCW.55: 3 residues within 4Å: Ligands: PCW.44, PCW.64, PCW.68 Ligand excluded by PLIP PCW.56: 4 residues within 4Å: Ligands: PCW.2, PCW.51, PCW.53, PCW.70 Ligand excluded by PLIP PCW.57: 4 residues within 4Å: Ligands: 17F.37, PCW.49, 17F.76, 17F.80 Ligand excluded by PLIP PCW.58: 5 residues within 4Å: Ligands: PCW.4, PCW.41, PCW.48, 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: 10 residues within 4Å: Ligands: PCW.6, PCW.11, PCW.16, PCW.24, PCW.48, PCW.52, PCW.58, PCW.61, PCW.62, PCW.63 Ligand excluded by PLIP PCW.61: 5 residues within 4Å: Ligands: PCW.41, PCW.48, PCW.58, PCW.59, PCW.60 Ligand excluded by PLIP PCW.62: 7 residues within 4Å: Ligands: PCW.24, 17F.39, PCW.54, PCW.60, PCW.67, PCW.72, 17F.78 Ligand excluded by PLIP PCW.63: 7 residues within 4Å: Ligands: PCW.6, PCW.11, PCW.28, PCW.42, PCW.60, PCW.67, 17F.75 Ligand excluded by PLIP PCW.64: 5 residues within 4Å: Ligands: PCW.5, 17F.38, PCW.44, PCW.53, PCW.55 Ligand excluded by PLIP PCW.65: 4 residues within 4Å: Chain B: A.89, L.100 Ligands: 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: 10 residues within 4Å: Ligands: PCW.25, PCW.26, PCW.28, PCW.29, PCW.62, PCW.63, PCW.66, PCW.69, 17F.75, 17F.78 Ligand excluded by PLIP PCW.68: 8 residues within 4Å: Ligands: 17F.33, 17F.40, PCW.43, PCW.44, PCW.53, PCW.55, PCW.69, PCW.70 Ligand excluded by PLIP PCW.69: 7 residues within 4Å: Ligands: PCW.26, PCW.42, PCW.43, PCW.44, PCW.67, PCW.68, 17F.75 Ligand excluded by PLIP PCW.70: 7 residues within 4Å: Ligands: PCW.43, PCW.46, PCW.51, PCW.53, PCW.56, PCW.68, PCW.71 Ligand excluded by PLIP PCW.71: 4 residues within 4Å: Ligands: PCW.46, PCW.47, PCW.51, PCW.70 Ligand excluded by PLIP PCW.72: 3 residues within 4Å: Ligands: PCW.54, PCW.62, 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-covalent)(Non-functional Binders)

17F.33: 9 residues within 4Å: Chain C: D.128, T.129, K.130 Ligands: PCW.4, PCW.7, PCW.32, 17F.35, PCW.44, PCW.68 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.128, C:K.130 Salt bridges: C:K.130, C:K.130 17F.34: 5 residues within 4Å: Ligands: PCW.9, PCW.13, PCW.14, PCW.30, 17F.40 No protein-ligand interaction detected (PLIP) 17F.35: 8 residues within 4Å: Chain C: Q.133, R.137, F.143 Ligands: PCW.1, PCW.7, PCW.32, 17F.33, 17F.38 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.133, C:F.143 Salt bridges: C:R.137 17F.36: 10 residues within 4Å: Chain C: K.177, K.179, K.186 Ligands: PCW.1, PCW.5, PCW.10, PCW.12, PCW.17, PCW.21, 17F.40 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.186 Salt bridges: C:K.177, C:K.177, C:K.179 17F.37: 8 residues within 4Å: Ligands: PCW.13, PCW.14, PCW.18, PCW.22, PCW.27, PCW.49, PCW.57, 17F.76 No protein-ligand interaction detected (PLIP) 17F.38: 7 residues within 4Å: Chain A: L.173 Chain C: R.137 Ligands: PCW.1, PCW.5, 17F.35, PCW.53, PCW.64 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.173 Salt bridges: C:R.137 17F.39: 10 residues within 4Å: Chain C: R.151 Ligands: PCW.4, PCW.6, PCW.15, PCW.16, PCW.20, PCW.24, PCW.28, PCW.42, PCW.62 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.151 17F.40: 11 residues within 4Å: Chain C: K.171, K.174, K.177 Ligands: PCW.1, PCW.12, PCW.26, PCW.30, 17F.34, 17F.36, PCW.68, 17F.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.171 Salt bridges: C:K.171, C:K.174, C:K.177 17F.73: 4 residues within 4Å: Ligands: PCW.8, PCW.47, PCW.49, 17F.76 No protein-ligand interaction detected (PLIP) 17F.74: 4 residues within 4Å: Ligands: 17F.40, PCW.45, 17F.75, 17F.79 No protein-ligand interaction detected (PLIP) 17F.75: 7 residues within 4Å: Ligands: PCW.42, PCW.43, PCW.63, PCW.67, PCW.69, 17F.74, 17F.79 No protein-ligand interaction detected (PLIP) 17F.76: 6 residues within 4Å: Ligands: PCW.27, 17F.37, PCW.47, PCW.49, PCW.57, 17F.73 No protein-ligand interaction detected (PLIP) 17F.77: 7 residues within 4Å: Chain B: L.192, Y.195, T.196, L.199 Ligands: PCW.41, PCW.44, PCW.59 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.192, B:Y.195, B:T.196, B:L.199 17F.78: 6 residues within 4Å: Ligands: PCW.50, PCW.62, PCW.66, PCW.67, PCW.72, 17F.79 No protein-ligand interaction detected (PLIP) 17F.79: 7 residues within 4Å: Ligands: PCW.23, PCW.45, PCW.66, 17F.74, 17F.75, 17F.78, 17F.80 No protein-ligand interaction detected (PLIP) 17F.80: 4 residues within 4Å: Ligands: PCW.49, PCW.57, PCW.65, 17F.79 No protein-ligand interaction detected (PLIP)

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

GDP.81: 20 residues within 4Å: Chain C: A.13, G.14, G.15, V.16, G.17, K.18, S.19, A.20, F.30, V.31, D.32, Y.34, P.36, N.118, K.119, D.121, L.122, S.147, A.148, K.149 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:A.13, C:G.15, C:V.16, C:G.17, C:K.18, C:S.19, C:S.19, C:S.19, C:A.20, C:D.32, C:N.118, C:K.119, C:K.119, C:A.148, C:K.149 Salt bridges: C:K.18, C:D.121 pi-Stacking: C:F.30, C:F.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.82: 5 residues within 4Å: Chain C: I.38, E.39, D.59, T.60, A.61 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:I.38, C:D.59, C:D.59, C:T.60

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Apolipoprotein A-I

GTPase KRas

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