SMTL ID : 6ccx.1

NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a 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-covalent)(Non-functional Binders)

PCW.1: 11 residues within 4Å: Chain B: Y.66, S.67, A.68 Ligands: PCW.12, PCW.13, PCW.23, 17F.37, PCW.61, PCW.64, PCW.70, PCW.74 Ligand excluded by PLIP PCW.2: 4 residues within 4Å: Ligands: PCW.20, PCW.24, PCW.25, PCW.71 Ligand excluded by PLIP PCW.3: 10 residues within 4Å: Chain B: D.175, K.178, K.179 Ligands: PCW.7, PCW.15, 17F.34, 17F.40, PCW.66, PCW.67, PCW.68 Ligand excluded by PLIP PCW.4: 5 residues within 4Å: Chain A: F.16 Ligands: PCW.5, PCW.22, PCW.28, PCW.58 Ligand excluded by PLIP PCW.5: 5 residues within 4Å: Ligands: PCW.4, PCW.14, PCW.33, PCW.77, 17F.82 Ligand excluded by PLIP PCW.6: 6 residues within 4Å: Ligands: PCW.9, PCW.17, PCW.19, PCW.26, PCW.32, 17F.37 Ligand excluded by PLIP PCW.7: 9 residues within 4Å: Ligands: PCW.3, PCW.10, 17F.34, 17F.36, 17F.39, PCW.54, PCW.63, PCW.68, 17F.81 Ligand excluded by PLIP PCW.8: 6 residues within 4Å: Ligands: PCW.10, PCW.15, PCW.42, PCW.52, PCW.66, PCW.68 Ligand excluded by PLIP PCW.9: 8 residues within 4Å: Ligands: PCW.6, PCW.19, 17F.37, 17F.41, PCW.53, PCW.64, PCW.75, PCW.76 Ligand excluded by PLIP PCW.10: 6 residues within 4Å: Ligands: PCW.7, PCW.8, 17F.36, PCW.54, PCW.68, 17F.81 Ligand excluded by PLIP PCW.12: 15 residues within 4Å: Chain B: R.75, T.76, K.106 Ligands: PCW.1, PCW.23, PCW.30, 17F.34, 17F.36, 17F.37, 17F.39, 17F.41, PCW.53, PCW.61, PCW.70, PCW.75 Ligand excluded by PLIP PCW.13: 9 residues within 4Å: Chain B: Y.66 Ligands: PCW.1, PCW.19, PCW.23, 17F.37, 17F.39, 17F.41, PCW.61, PCW.70 Ligand excluded by PLIP PCW.14: 11 residues within 4Å: Chain B: S.173 Ligands: PCW.5, PCW.15, PCW.18, PCW.22, PCW.28, PCW.31, 17F.34, 17F.40, PCW.42, PCW.69 Ligand excluded by PLIP PCW.15: 9 residues within 4Å: Chain B: M.172 Ligands: PCW.3, PCW.8, PCW.14, PCW.22, 17F.36, PCW.42, PCW.66, PCW.74 Ligand excluded by PLIP PCW.16: 10 residues within 4Å: Chain B: M.3, E.5, L.54 Ligands: PCW.18, PCW.21, PCW.30, PCW.31, PCW.32, 17F.35, PCW.44 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Ligands: PCW.6, PCW.19, PCW.26, 17F.37, PCW.49 Ligand excluded by PLIP PCW.18: 15 residues within 4Å: Chain B: T.4 Ligands: PCW.14, PCW.16, PCW.22, PCW.28, PCW.29, PCW.31, 17F.35, 17F.40, PCW.42, PCW.43, 17F.45, PCW.67, PCW.69, 17F.79 Ligand excluded by PLIP PCW.19: 14 residues within 4Å: Chain B: E.39, S.41 Ligands: PCW.6, PCW.9, PCW.13, PCW.17, PCW.23, PCW.26, PCW.32, 17F.37, 17F.38, EWS.48, PCW.56, PCW.75 Ligand excluded by PLIP PCW.20: 9 residues within 4Å: Ligands: PCW.2, PCW.24, PCW.27, 17F.38, PCW.57, PCW.59, PCW.65, PCW.71, 17F.83 Ligand excluded by PLIP PCW.21: 9 residues within 4Å: Chain B: M.3, R.43, Q.45, L.54 Ligands: PCW.16, PCW.27, PCW.32, 17F.35, 17F.38 Ligand excluded by PLIP PCW.22: 9 residues within 4Å: Chain B: S.173 Ligands: PCW.4, PCW.14, PCW.15, PCW.18, PCW.28, 17F.40, PCW.67, PCW.69 Ligand excluded by PLIP PCW.23: 13 residues within 4Å: Chain B: Y.66, A.68, D.71, Q.72, R.75, R.104 Ligands: PCW.1, PCW.12, PCW.13, PCW.19, 17F.37, 17F.41, PCW.61 Ligand excluded by PLIP PCW.24: 8 residues within 4Å: Ligands: PCW.2, PCW.20, PCW.25, PCW.27, 17F.38, PCW.59, 17F.78, 17F.83 Ligand excluded by PLIP PCW.25: 6 residues within 4Å: Ligands: PCW.2, PCW.24, PCW.27, PCW.51, PCW.60, 17F.82 Ligand excluded by PLIP PCW.26: 8 residues within 4Å: Ligands: PCW.6, PCW.17, PCW.19, PCW.32, PCW.49, PCW.56, PCW.57, PCW.76 Ligand excluded by PLIP PCW.27: 9 residues within 4Å: Ligands: PCW.20, PCW.21, PCW.24, PCW.25, 17F.35, 17F.38, PCW.59, PCW.65, 17F.82 Ligand excluded by PLIP PCW.28: 9 residues within 4Å: Ligands: PCW.4, PCW.14, PCW.18, PCW.22, PCW.29, 17F.40, PCW.43, PCW.67, PCW.77 Ligand excluded by PLIP PCW.29: 7 residues within 4Å: Ligands: PCW.18, PCW.28, PCW.33, PCW.51, PCW.73, PCW.77, 17F.82 Ligand excluded by PLIP PCW.30: 17 residues within 4Å: Chain B: E.5, K.7, T.76, E.78, K.169 Ligands: PCW.12, PCW.16, PCW.31, 17F.34, 17F.35, 17F.37, 17F.41, PCW.44, PCW.53, PCW.73, PCW.74, 17F.79 Ligand excluded by PLIP PCW.31: 13 residues within 4Å: Chain B: K.169, M.172, S.173 Ligands: PCW.14, PCW.16, PCW.18, PCW.30, PCW.42, PCW.43, PCW.44, 17F.45, PCW.52, PCW.73 Ligand excluded by PLIP PCW.32: 16 residues within 4Å: Chain B: E.5, K.7, R.43, D.56 Ligands: PCW.6, PCW.16, PCW.19, PCW.21, PCW.26, 17F.35, 17F.37, 17F.38, 17F.41, EWS.48, PCW.56, PCW.75 Ligand excluded by PLIP PCW.33: 5 residues within 4Å: Ligands: PCW.5, PCW.29, PCW.51, PCW.77, 17F.82 Ligand excluded by PLIP PCW.42: 11 residues within 4Å: Ligands: PCW.8, PCW.14, PCW.15, PCW.18, PCW.31, 17F.40, PCW.44, PCW.52, PCW.66, PCW.67, PCW.69 Ligand excluded by PLIP PCW.43: 7 residues within 4Å: Ligands: PCW.18, PCW.28, PCW.31, 17F.45, PCW.52, PCW.67, PCW.73 Ligand excluded by PLIP PCW.44: 11 residues within 4Å: Ligands: PCW.16, PCW.30, PCW.31, 17F.34, 17F.35, PCW.42, PCW.52, PCW.53, PCW.54, PCW.73, PCW.74 Ligand excluded by PLIP PCW.49: 5 residues within 4Å: Ligands: PCW.17, PCW.26, PCW.50, PCW.56, 17F.78 Ligand excluded by PLIP PCW.50: 4 residues within 4Å: Ligands: 17F.38, PCW.49, PCW.57, 17F.78 Ligand excluded by PLIP PCW.51: 5 residues within 4Å: Ligands: PCW.25, PCW.29, PCW.33, PCW.60, PCW.73 Ligand excluded by PLIP PCW.52: 6 residues within 4Å: Ligands: PCW.8, PCW.31, 17F.40, PCW.42, PCW.43, PCW.44 Ligand excluded by PLIP PCW.53: 8 residues within 4Å: Ligands: PCW.9, PCW.12, PCW.30, 17F.41, PCW.44, 17F.45, PCW.55, PCW.74 Ligand excluded by PLIP PCW.54: 10 residues within 4Å: Ligands: PCW.7, PCW.10, 17F.34, 17F.36, PCW.44, PCW.61, PCW.63, PCW.70, PCW.74, 17F.81 Ligand excluded by PLIP PCW.55: 8 residues within 4Å: Ligands: 17F.11, 17F.35, 17F.45, PCW.53, PCW.57, PCW.59, PCW.76, 17F.79 Ligand excluded by PLIP PCW.56: 7 residues within 4Å: Ligands: PCW.19, PCW.26, PCW.32, PCW.49, PCW.57, PCW.76, 17F.78 Ligand excluded by PLIP PCW.57: 10 residues within 4Å: Ligands: PCW.20, PCW.26, 17F.38, PCW.50, PCW.55, PCW.56, PCW.59, PCW.65, 17F.78, 17F.80 Ligand excluded by PLIP PCW.58: 4 residues within 4Å: Ligands: PCW.4, PCW.62, PCW.66, PCW.67 Ligand excluded by PLIP PCW.59: 10 residues within 4Å: Ligands: PCW.20, PCW.24, PCW.27, 17F.35, 17F.38, PCW.55, PCW.57, PCW.65, PCW.76, 17F.83 Ligand excluded by PLIP PCW.60: 3 residues within 4Å: Ligands: PCW.25, PCW.51, 17F.82 Ligand excluded by PLIP PCW.61: 12 residues within 4Å: Ligands: PCW.1, PCW.12, PCW.13, PCW.23, 17F.39, 17F.41, PCW.54, PCW.63, PCW.64, PCW.70, PCW.74, PCW.75 Ligand excluded by PLIP PCW.62: 3 residues within 4Å: Ligands: PCW.58, PCW.69, PCW.77 Ligand excluded by PLIP PCW.63: 7 residues within 4Å: Ligands: PCW.7, 17F.36, 17F.39, PCW.54, PCW.61, PCW.70, PCW.74 Ligand excluded by PLIP PCW.64: 4 residues within 4Å: Ligands: PCW.1, PCW.9, PCW.61, PCW.70 Ligand excluded by PLIP PCW.65: 8 residues within 4Å: Ligands: 17F.11, PCW.20, PCW.27, 17F.38, PCW.57, PCW.59, 17F.80, 17F.83 Ligand excluded by PLIP PCW.66: 6 residues within 4Å: Ligands: PCW.3, PCW.8, PCW.15, PCW.42, PCW.58, PCW.68 Ligand excluded by PLIP PCW.67: 9 residues within 4Å: Ligands: PCW.3, PCW.18, PCW.22, PCW.28, PCW.42, PCW.43, PCW.58, PCW.69, PCW.77 Ligand excluded by PLIP PCW.68: 5 residues within 4Å: Ligands: PCW.3, PCW.7, PCW.8, PCW.10, PCW.66 Ligand excluded by PLIP PCW.69: 9 residues within 4Å: Ligands: PCW.14, PCW.18, PCW.22, PCW.42, PCW.62, PCW.67, PCW.73, PCW.77, 17F.82 Ligand excluded by PLIP PCW.70: 9 residues within 4Å: Ligands: PCW.1, PCW.12, PCW.13, 17F.36, 17F.39, PCW.54, PCW.61, PCW.63, PCW.64 Ligand excluded by PLIP PCW.71: 4 residues within 4Å: Chain C: K.92 Ligands: PCW.2, PCW.20, 17F.83 Ligand excluded by PLIP PCW.72: 4 residues within 4Å: Ligands: 17F.11, PCW.73, 17F.82, 17F.83 Ligand excluded by PLIP PCW.73: 11 residues within 4Å: Ligands: PCW.29, PCW.30, PCW.31, PCW.43, PCW.44, 17F.45, PCW.51, PCW.69, PCW.72, 17F.79, 17F.82 Ligand excluded by PLIP PCW.74: 12 residues within 4Å: Ligands: PCW.1, PCW.15, PCW.30, 17F.34, 17F.36, 17F.37, PCW.44, PCW.53, PCW.54, PCW.61, PCW.63, PCW.75 Ligand excluded by PLIP PCW.75: 9 residues within 4Å: Ligands: PCW.9, PCW.12, PCW.19, PCW.32, 17F.37, 17F.41, PCW.61, PCW.74, PCW.76 Ligand excluded by PLIP PCW.76: 7 residues within 4Å: Ligands: PCW.9, PCW.26, 17F.37, PCW.55, PCW.56, PCW.59, PCW.75 Ligand excluded by PLIP PCW.77: 8 residues within 4Å: Ligands: PCW.5, PCW.28, PCW.29, PCW.33, PCW.62, PCW.67, PCW.69, 17F.82 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.11: 6 residues within 4Å: Ligands: PCW.55, PCW.65, PCW.72, 17F.79, 17F.82, 17F.83 No protein-ligand interaction detected (PLIP) 17F.34: 10 residues within 4Å: Chain B: K.179 Ligands: PCW.3, PCW.7, PCW.12, PCW.14, PCW.30, 17F.36, PCW.44, PCW.54, PCW.74 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.179 17F.35: 14 residues within 4Å: Chain B: R.43 Ligands: PCW.16, PCW.18, PCW.21, PCW.27, PCW.30, PCW.32, 17F.38, 17F.41, PCW.44, 17F.45, PCW.55, PCW.59, 17F.79 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.43, B:R.43 17F.36: 11 residues within 4Å: Chain B: M.172 Ligands: PCW.7, PCW.10, PCW.12, PCW.15, 17F.34, 17F.39, PCW.54, PCW.63, PCW.70, PCW.74 No protein-ligand interaction detected (PLIP) 17F.37: 18 residues within 4Å: Chain B: A.68, M.69, Q.72 Ligands: PCW.1, PCW.6, PCW.9, PCW.12, PCW.13, PCW.17, PCW.19, PCW.23, PCW.30, PCW.32, 17F.41, EWS.48, PCW.74, PCW.75, PCW.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.69, B:Q.72 17F.38: 12 residues within 4Å: Chain B: R.43 Ligands: PCW.19, PCW.20, PCW.21, PCW.24, PCW.27, PCW.32, 17F.35, PCW.50, PCW.57, PCW.59, PCW.65 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.43 17F.39: 8 residues within 4Å: Chain B: D.107 Ligands: PCW.7, PCW.12, PCW.13, 17F.36, PCW.61, PCW.63, PCW.70 No protein-ligand interaction detected (PLIP) 17F.40: 7 residues within 4Å: Ligands: PCW.3, PCW.14, PCW.18, PCW.22, PCW.28, PCW.42, PCW.52 No protein-ligand interaction detected (PLIP) 17F.41: 15 residues within 4Å: Chain B: Q.72, R.75, T.76 Ligands: PCW.9, PCW.12, PCW.13, PCW.23, PCW.30, PCW.32, 17F.35, 17F.37, EWS.48, PCW.53, PCW.61, PCW.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.72 17F.45: 8 residues within 4Å: Ligands: PCW.18, PCW.31, 17F.35, PCW.43, PCW.53, PCW.55, PCW.73, 17F.79 No protein-ligand interaction detected (PLIP) 17F.78: 6 residues within 4Å: Ligands: PCW.24, PCW.49, PCW.50, PCW.56, PCW.57, 17F.80 No protein-ligand interaction detected (PLIP) 17F.79: 7 residues within 4Å: Ligands: 17F.11, PCW.18, PCW.30, 17F.35, 17F.45, PCW.55, PCW.73 No protein-ligand interaction detected (PLIP) 17F.80: 5 residues within 4Å: Chain C: Y.74 Ligands: PCW.57, PCW.65, 17F.78, 17F.83 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.74 17F.81: 3 residues within 4Å: Ligands: PCW.7, PCW.10, PCW.54 No protein-ligand interaction detected (PLIP) 17F.82: 11 residues within 4Å: Ligands: PCW.5, 17F.11, PCW.25, PCW.27, PCW.29, PCW.33, PCW.60, PCW.69, PCW.72, PCW.73, PCW.77 No protein-ligand interaction detected (PLIP) 17F.83: 8 residues within 4Å: Ligands: 17F.11, PCW.20, PCW.24, PCW.59, PCW.65, PCW.71, PCW.72, 17F.80 No protein-ligand interaction detected (PLIP)

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

GNP.46: 23 residues within 4Å: Chain B: A.13, V.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, D.121, L.122, S.147, A.148, K.149 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.13, B:G.15, B:G.17, B:K.18, B:S.19, B:S.19, B:S.19, B:A.20, B:V.31, B:D.32, B:D.35, B:N.118, B:K.119, B:K.119, B:A.148, B:K.149 Salt bridges: B:D.121 pi-Stacking: B:F.30 pi-Cation interactions: B:K.119

1 x MG: MAGNESIUM ION(Non-covalent)

MG.47: 4 residues within 4Å: Chain B: S.19, T.37, D.40, D.59 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.37, B:D.40, B:D.59

1 x EWS: (2R,4S)-4-[(5-bromo-1H-indole-3-carbonyl)amino]-2-[(4-chlorophenyl)methyl]piperidin-1-ium(Non-covalent)

EWS.48: 18 residues within 4Å: Chain B: E.5, K.7, L.8, V.9, E.39, D.56, L.58, M.69, Q.72, Y.73, M.74, R.75, T.76, G.77 Ligands: PCW.19, PCW.32, 17F.37, 17F.41 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.7, B:D.56, B:L.58, B:Y.73, B:T.76 Hydrogen bonds: B:L.8, B:Q.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, Z. et al., Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. Cell Chem Biol (2018)

Release Date

2018-09-05

Peptides

Apolipoprotein A-I: AC
GTPase KRas: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

Apolipoprotein A-I

GTPase KRas

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