SMTL ID : 7rse.1

NMR-driven structure of the KRAS4B-G12D "alpha-beta" dimer on a lipid bilayer nanodisc

Coordinates

PDB Format

Method

SOLUTION NMR

Oligo State

hetero-2-2-mer

Ligands

2 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 24 residues within 4Å: Chain A: G.13, V.14, G.15, K.16, S.17, A.18, E.31, Y.32, D.33, P.34, T.35, D.57, T.58, A.59, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147, T.148 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:A.18, A:D.33, A:D.33, A:T.35, A:G.60, A:N.116, A:K.117, A:S.145, A:S.145, A:A.146, A:K.147, A:K.147 Salt bridges: A:D.119 GSP.18: 19 residues within 4Å: Chain B: A.11, D.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, Y.32, D.57, Q.61, N.116, K.117, D.119, L.120, S.145, K.147 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:S.17, B:A.18, B:N.116, B:K.117 Salt bridges: B:D.119

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.17, D.33, T.35, D.57 Ligands: GSP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.17, A:T.35, A:D.57 MG.19: 3 residues within 4Å: Chain B: S.17, D.57 Ligands: GSP.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.17

128 x 7Q9: [(2~{R})-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] (~{Z})-octadec-9-enoate(Non-functional Binders)(Non-covalent)

7Q9.3: 4 residues within 4Å: Ligands: 7Q9.5, 7Q9.7, 7Q9.21, 7Q9.92 No protein-ligand interaction detected (PLIP) 7Q9.4: 5 residues within 4Å: Chain B: S.181 Ligands: 17F.8, 17F.25, 17F.97, 7Q9.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.181 7Q9.5: 9 residues within 4Å: Ligands: 7Q9.3, 7Q9.7, 7Q9.21, 7Q9.26, 7Q9.40, 7Q9.41, 7Q9.92, 7Q9.100, 7Q9.106 No protein-ligand interaction detected (PLIP) 7Q9.6: 5 residues within 4Å: Ligands: 7Q9.9, 7Q9.10, 7Q9.12, 7Q9.94, 17F.97 No protein-ligand interaction detected (PLIP) 7Q9.7: 4 residues within 4Å: Ligands: 7Q9.3, 7Q9.5, 7Q9.41, 7Q9.44 No protein-ligand interaction detected (PLIP) 7Q9.9: 7 residues within 4Å: Ligands: 7Q9.6, 17F.8, 7Q9.12, 17F.14, 7Q9.108, 7Q9.109, 7Q9.125 No protein-ligand interaction detected (PLIP) 7Q9.10: 5 residues within 4Å: Ligands: 7Q9.6, 7Q9.12, 7Q9.15, 7Q9.16, 7Q9.112 No protein-ligand interaction detected (PLIP) 7Q9.11: 9 residues within 4Å: Chain B: K.184 Ligands: 17F.8, 7Q9.13, 7Q9.17, 17F.31, 7Q9.37, 7Q9.55, 7Q9.131, 7Q9.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.184 7Q9.12: 8 residues within 4Å: Chain A: K.176, K.177 Ligands: 7Q9.6, 7Q9.9, 7Q9.10, 17F.14, 7Q9.108, 7Q9.112 No protein-ligand interaction detected (PLIP) 7Q9.13: 6 residues within 4Å: Ligands: 17F.8, 7Q9.11, 7Q9.17, 7Q9.55, 7Q9.109, 7Q9.116 No protein-ligand interaction detected (PLIP) 7Q9.15: 5 residues within 4Å: Ligands: 7Q9.10, 7Q9.16, 17F.71, 7Q9.73, 7Q9.126 No protein-ligand interaction detected (PLIP) 7Q9.16: 7 residues within 4Å: Chain A: T.183 Ligands: 7Q9.10, 7Q9.15, 7Q9.44, 7Q9.60, 7Q9.73, 7Q9.84 No protein-ligand interaction detected (PLIP) 7Q9.17: 6 residues within 4Å: Ligands: 7Q9.11, 7Q9.13, 7Q9.81, 17F.83, 7Q9.125, 7Q9.131 No protein-ligand interaction detected (PLIP) 7Q9.20: 7 residues within 4Å: Chain B: K.178 Ligands: 7Q9.21, 7Q9.22, 7Q9.23, 17F.25, 7Q9.29, 17F.87 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.178, B:K.178 7Q9.21: 7 residues within 4Å: Ligands: 7Q9.3, 7Q9.5, 7Q9.20, 7Q9.22, 7Q9.24, 7Q9.26, 17F.87 No protein-ligand interaction detected (PLIP) 7Q9.22: 6 residues within 4Å: Ligands: 7Q9.20, 7Q9.21, 7Q9.23, 7Q9.24, 7Q9.28, 7Q9.88 No protein-ligand interaction detected (PLIP) 7Q9.23: 9 residues within 4Å: Chain B: K.177, K.178 Ligands: 7Q9.20, 7Q9.22, 17F.25, 7Q9.27, 7Q9.29, 17F.91, 7Q9.96 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.177 7Q9.24: 7 residues within 4Å: Ligands: 7Q9.21, 7Q9.22, 7Q9.26, 7Q9.28, 17F.38, 17F.87, 7Q9.89 No protein-ligand interaction detected (PLIP) 7Q9.26: 6 residues within 4Å: Ligands: 7Q9.5, 7Q9.21, 7Q9.24, 7Q9.39, 7Q9.40, 7Q9.42 No protein-ligand interaction detected (PLIP) 7Q9.27: 3 residues within 4Å: Ligands: 7Q9.23, 7Q9.28, 7Q9.30 No protein-ligand interaction detected (PLIP) 7Q9.28: 6 residues within 4Å: Ligands: 7Q9.22, 7Q9.24, 7Q9.27, 17F.32, 17F.38, 17F.95 No protein-ligand interaction detected (PLIP) 7Q9.29: 5 residues within 4Å: Ligands: 7Q9.20, 7Q9.23, 17F.25, 7Q9.30, 7Q9.34 No protein-ligand interaction detected (PLIP) 7Q9.30: 7 residues within 4Å: Ligands: 7Q9.27, 7Q9.29, 7Q9.33, 7Q9.35, 7Q9.51, 7Q9.85, 7Q9.111 No protein-ligand interaction detected (PLIP) 7Q9.33: 7 residues within 4Å: Ligands: 7Q9.30, 17F.32, 7Q9.51, 7Q9.52, 7Q9.56, 7Q9.107, 7Q9.129 No protein-ligand interaction detected (PLIP) 7Q9.34: 5 residues within 4Å: Ligands: 17F.25, 7Q9.29, 17F.31, 17F.36, 7Q9.59 No protein-ligand interaction detected (PLIP) 7Q9.35: 4 residues within 4Å: Ligands: 7Q9.30, 7Q9.51, 7Q9.68, 7Q9.79 No protein-ligand interaction detected (PLIP) 7Q9.37: 7 residues within 4Å: Ligands: 7Q9.11, 17F.31, 17F.36, 7Q9.55, 17F.70, 7Q9.80, 7Q9.136 No protein-ligand interaction detected (PLIP) 7Q9.39: 5 residues within 4Å: Ligands: 7Q9.26, 7Q9.42, 7Q9.45, 7Q9.99, 17F.105 No protein-ligand interaction detected (PLIP) 7Q9.40: 7 residues within 4Å: Ligands: 7Q9.5, 7Q9.26, 7Q9.41, 7Q9.42, 17F.48, 7Q9.100, 7Q9.106 No protein-ligand interaction detected (PLIP) 7Q9.41: 5 residues within 4Å: Ligands: 7Q9.5, 7Q9.7, 7Q9.40, 7Q9.44, 17F.53 No protein-ligand interaction detected (PLIP) 7Q9.42: 6 residues within 4Å: Ligands: 7Q9.26, 7Q9.39, 7Q9.40, 17F.48, 7Q9.50, 17F.105 No protein-ligand interaction detected (PLIP) 7Q9.43: 6 residues within 4Å: Ligands: 17F.32, 17F.54, 7Q9.57, 7Q9.123, 17F.127, 7Q9.128 No protein-ligand interaction detected (PLIP) 7Q9.44: 8 residues within 4Å: Chain A: T.183, K.184 Ligands: 7Q9.7, 7Q9.16, 7Q9.41, 17F.53, 7Q9.106, 17F.124 No protein-ligand interaction detected (PLIP) 7Q9.45: 6 residues within 4Å: Ligands: 17F.38, 7Q9.39, 7Q9.46, 7Q9.58, 17F.104, 7Q9.121 No protein-ligand interaction detected (PLIP) 7Q9.46: 6 residues within 4Å: Ligands: 17F.38, 7Q9.45, 7Q9.57, 7Q9.58, 7Q9.62, 7Q9.121 No protein-ligand interaction detected (PLIP) 7Q9.49: 6 residues within 4Å: Ligands: 7Q9.50, 17F.65, 7Q9.67, 7Q9.69, 7Q9.122, 7Q9.138 No protein-ligand interaction detected (PLIP) 7Q9.50: 6 residues within 4Å: Ligands: 7Q9.42, 17F.48, 7Q9.49, 7Q9.63, 17F.65, 7Q9.134 No protein-ligand interaction detected (PLIP) 7Q9.51: 6 residues within 4Å: Ligands: 7Q9.30, 7Q9.33, 7Q9.35, 7Q9.56, 7Q9.68, 7Q9.129 No protein-ligand interaction detected (PLIP) 7Q9.52: 7 residues within 4Å: Ligands: 17F.32, 7Q9.33, 17F.54, 7Q9.56, 7Q9.78, 7Q9.107, 7Q9.129 No protein-ligand interaction detected (PLIP) 7Q9.55: 5 residues within 4Å: Ligands: 7Q9.11, 7Q9.13, 7Q9.37, 17F.70, 7Q9.74 No protein-ligand interaction detected (PLIP) 7Q9.56: 6 residues within 4Å: Ligands: 7Q9.33, 7Q9.51, 7Q9.52, 7Q9.77, 7Q9.78, 7Q9.150 No protein-ligand interaction detected (PLIP) 7Q9.57: 8 residues within 4Å: Ligands: 7Q9.43, 7Q9.46, 17F.54, 7Q9.62, 7Q9.75, 7Q9.123, 7Q9.128, 7Q9.162 No protein-ligand interaction detected (PLIP) 7Q9.58: 6 residues within 4Å: Chain C: R.108 Chain D: W.67 Ligands: 7Q9.45, 7Q9.46, 7Q9.62, 7Q9.67 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:R.108, D:W.67 7Q9.59: 4 residues within 4Å: Ligands: 7Q9.34, 17F.36, 7Q9.79, 7Q9.82 No protein-ligand interaction detected (PLIP) 7Q9.60: 6 residues within 4Å: Chain C: K.53 Chain D: Y.125 Ligands: 7Q9.16, 7Q9.72, 7Q9.84, 7Q9.143 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.53 Hydrophobic interactions: D:Y.125 7Q9.61: 3 residues within 4Å: Ligands: 17F.47, 17F.48, 7Q9.63 No protein-ligand interaction detected (PLIP) 7Q9.62: 4 residues within 4Å: Chain C: R.112 Ligands: 7Q9.46, 7Q9.57, 7Q9.58 No protein-ligand interaction detected (PLIP) 7Q9.63: 6 residues within 4Å: Chain C: V.78, R.82 Ligands: 17F.48, 7Q9.50, 7Q9.61, 7Q9.86 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.78 7Q9.66: 7 residues within 4Å: Chain C: R.130, L.133, A.134 Chain D: L.49 Ligands: 17F.54, 7Q9.75, 7Q9.147 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.49, C:R.130, C:L.133, C:L.133, C:A.134 7Q9.67: 6 residues within 4Å: Chain C: Q.97, E.105, R.108 Ligands: 7Q9.49, 7Q9.58, 7Q9.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.97 7Q9.68: 6 residues within 4Å: Chain C: Y.151, H.152, A.155 Ligands: 7Q9.35, 7Q9.51, 7Q9.77 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.155, C:A.155 7Q9.69: 8 residues within 4Å: Chain C: A.89, R.90, L.93, H.94, Q.97 Ligands: 7Q9.49, 17F.65, 7Q9.67 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.90, C:L.93 Salt bridges: C:H.94, C:H.94 7Q9.72: 9 residues within 4Å: Chain C: Q.57, L.60, D.61, Q.64 Ligands: 7Q9.60, 17F.64, 17F.124, 7Q9.143, 17F.160 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.60 7Q9.73: 6 residues within 4Å: Chain C: E.39, R.42 Ligands: 7Q9.15, 7Q9.16, 17F.71, 7Q9.84 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.39 7Q9.74: 7 residues within 4Å: Chain C: L.192, Y.195, T.196, L.199 Ligands: 7Q9.55, 17F.83, 7Q9.157 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.192, C:Y.195, C:T.196, C:L.199, C:L.199 7Q9.75: 4 residues within 4Å: Chain C: S.126 Ligands: 17F.54, 7Q9.57, 7Q9.66 No protein-ligand interaction detected (PLIP) 7Q9.76: 3 residues within 4Å: Chain C: W.31 Ligands: 17F.14, 17F.71 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.31 7Q9.77: 5 residues within 4Å: Chain C: L.148, H.152 Ligands: 7Q9.56, 7Q9.68, 7Q9.163 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.148, C:L.148 7Q9.78: 4 residues within 4Å: Chain C: K.141 Ligands: 7Q9.52, 17F.54, 7Q9.56 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.141 Salt bridges: C:K.141, C:K.141 7Q9.79: 6 residues within 4Å: Chain C: L.159, S.160, L.162, S.163 Ligands: 7Q9.35, 7Q9.59 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.159, C:L.159, C:L.162 7Q9.80: 5 residues within 4Å: Ligands: 17F.36, 7Q9.37, 17F.70, 7Q9.155, 7Q9.161 No protein-ligand interaction detected (PLIP) 7Q9.81: 7 residues within 4Å: Chain C: F.16, S.17, K.18, R.20 Ligands: 7Q9.17, 17F.83, 7Q9.151 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.16 7Q9.82: 3 residues within 4Å: Ligands: 17F.36, 7Q9.59, 7Q9.155 No protein-ligand interaction detected (PLIP) 7Q9.84: 6 residues within 4Å: Chain C: L.49, E.50, K.53 Ligands: 7Q9.16, 7Q9.60, 7Q9.73 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.49, C:L.49, C:E.50, C:E.50, C:K.53 7Q9.85: 6 residues within 4Å: Ligands: 7Q9.30, 7Q9.98, 7Q9.102, 7Q9.111, 7Q9.117, 7Q9.133 No protein-ligand interaction detected (PLIP) 7Q9.86: 6 residues within 4Å: Chain C: Y.74 Chain D: R.108 Ligands: 7Q9.63, 7Q9.118, 7Q9.137, 17F.142 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:R.108, C:Y.74 7Q9.88: 4 residues within 4Å: Ligands: 7Q9.22, 17F.87, 17F.93, 17F.95 No protein-ligand interaction detected (PLIP) 7Q9.89: 6 residues within 4Å: Ligands: 7Q9.24, 17F.87, 7Q9.92, 17F.93, 7Q9.99, 7Q9.100 No protein-ligand interaction detected (PLIP) 7Q9.90: 5 residues within 4Å: Ligands: 17F.8, 17F.87, 17F.97, 7Q9.98, 7Q9.101 No protein-ligand interaction detected (PLIP) 7Q9.92: 6 residues within 4Å: Ligands: 7Q9.3, 7Q9.5, 7Q9.89, 7Q9.94, 7Q9.100, 17F.103 No protein-ligand interaction detected (PLIP) 7Q9.94: 5 residues within 4Å: Ligands: 7Q9.6, 7Q9.92, 17F.97, 17F.103, 7Q9.112 No protein-ligand interaction detected (PLIP) 7Q9.96: 6 residues within 4Å: Ligands: 7Q9.23, 17F.91, 17F.95, 7Q9.102, 7Q9.107, 7Q9.111 No protein-ligand interaction detected (PLIP) 7Q9.98: 7 residues within 4Å: Ligands: 17F.25, 7Q9.85, 7Q9.90, 17F.91, 7Q9.101, 7Q9.102, 7Q9.113 No protein-ligand interaction detected (PLIP) 7Q9.99: 6 residues within 4Å: Ligands: 7Q9.39, 7Q9.89, 17F.93, 17F.104, 17F.105, 7Q9.115 No protein-ligand interaction detected (PLIP) 7Q9.100: 6 residues within 4Å: Ligands: 7Q9.5, 7Q9.40, 7Q9.89, 7Q9.92, 7Q9.106, 17F.114 No protein-ligand interaction detected (PLIP) 7Q9.101: 5 residues within 4Å: Ligands: 7Q9.90, 17F.97, 7Q9.98, 7Q9.113, 7Q9.116 No protein-ligand interaction detected (PLIP) 7Q9.102: 6 residues within 4Å: Ligands: 7Q9.85, 17F.91, 7Q9.96, 7Q9.98, 7Q9.111, 7Q9.117 No protein-ligand interaction detected (PLIP) 7Q9.106: 7 residues within 4Å: Ligands: 7Q9.5, 7Q9.40, 7Q9.44, 7Q9.100, 17F.103, 7Q9.119, 17F.124 No protein-ligand interaction detected (PLIP) 7Q9.107: 8 residues within 4Å: Ligands: 17F.32, 7Q9.33, 7Q9.52, 7Q9.96, 7Q9.110, 7Q9.111, 7Q9.128, 7Q9.129 No protein-ligand interaction detected (PLIP) 7Q9.108: 8 residues within 4Å: Ligands: 7Q9.4, 17F.8, 7Q9.9, 7Q9.12, 17F.97, 7Q9.109, 7Q9.112, 7Q9.125 No protein-ligand interaction detected (PLIP) 7Q9.109: 7 residues within 4Å: Ligands: 17F.8, 7Q9.9, 7Q9.13, 17F.97, 7Q9.108, 7Q9.125, 7Q9.131 No protein-ligand interaction detected (PLIP) 7Q9.110: 5 residues within 4Å: Ligands: 17F.95, 17F.104, 7Q9.107, 17F.127, 7Q9.128 No protein-ligand interaction detected (PLIP) 7Q9.111: 7 residues within 4Å: Ligands: 7Q9.30, 7Q9.85, 7Q9.96, 7Q9.102, 7Q9.107, 7Q9.117, 7Q9.130 No protein-ligand interaction detected (PLIP) 7Q9.112: 7 residues within 4Å: Ligands: 7Q9.10, 7Q9.12, 7Q9.94, 17F.103, 7Q9.108, 7Q9.120, 7Q9.135 No protein-ligand interaction detected (PLIP) 7Q9.113: 5 residues within 4Å: Ligands: 17F.31, 7Q9.98, 7Q9.101, 7Q9.116, 7Q9.132 No protein-ligand interaction detected (PLIP) 7Q9.115: 5 residues within 4Å: Ligands: 17F.65, 7Q9.99, 17F.105, 17F.114, 7Q9.138 No protein-ligand interaction detected (PLIP) 7Q9.116: 4 residues within 4Å: Ligands: 7Q9.13, 7Q9.101, 7Q9.113, 7Q9.131 No protein-ligand interaction detected (PLIP) 7Q9.117: 5 residues within 4Å: Ligands: 7Q9.85, 7Q9.102, 7Q9.111, 7Q9.130, 7Q9.139 No protein-ligand interaction detected (PLIP) 7Q9.118: 7 residues within 4Å: Ligands: 17F.47, 17F.53, 7Q9.86, 17F.114, 17F.124, 7Q9.137, 17F.142 No protein-ligand interaction detected (PLIP) 7Q9.119: 6 residues within 4Å: Ligands: 17F.103, 7Q9.106, 7Q9.120, 17F.124, 7Q9.143, 17F.160 No protein-ligand interaction detected (PLIP) 7Q9.120: 5 residues within 4Å: Ligands: 7Q9.112, 7Q9.119, 7Q9.135, 17F.141, 7Q9.153 No protein-ligand interaction detected (PLIP) 7Q9.121: 5 residues within 4Å: Ligands: 7Q9.45, 7Q9.46, 17F.104, 17F.105, 7Q9.122 No protein-ligand interaction detected (PLIP) 7Q9.122: 5 residues within 4Å: Ligands: 7Q9.49, 17F.105, 7Q9.121, 7Q9.138, 7Q9.140 No protein-ligand interaction detected (PLIP) 7Q9.123: 7 residues within 4Å: Ligands: 7Q9.43, 7Q9.57, 17F.104, 17F.127, 7Q9.146, 7Q9.152, 7Q9.162 No protein-ligand interaction detected (PLIP) 7Q9.125: 7 residues within 4Å: Ligands: 7Q9.9, 7Q9.17, 7Q9.108, 7Q9.109, 7Q9.126, 7Q9.131, 7Q9.154 No protein-ligand interaction detected (PLIP) 7Q9.126: 7 residues within 4Å: Ligands: 17F.14, 7Q9.15, 7Q9.125, 7Q9.135, 7Q9.149, 7Q9.154, 7Q9.159 No protein-ligand interaction detected (PLIP) 7Q9.128: 9 residues within 4Å: Ligands: 7Q9.43, 17F.54, 7Q9.57, 7Q9.107, 7Q9.110, 17F.127, 7Q9.129, 7Q9.147, 7Q9.162 No protein-ligand interaction detected (PLIP) 7Q9.129: 8 residues within 4Å: Ligands: 7Q9.33, 7Q9.51, 7Q9.52, 7Q9.107, 7Q9.128, 7Q9.130, 7Q9.145, 7Q9.150 No protein-ligand interaction detected (PLIP) 7Q9.130: 5 residues within 4Å: Ligands: 7Q9.111, 7Q9.117, 7Q9.129, 7Q9.150, 7Q9.163 No protein-ligand interaction detected (PLIP) 7Q9.131: 6 residues within 4Å: Ligands: 7Q9.11, 7Q9.17, 7Q9.109, 7Q9.116, 7Q9.125, 7Q9.151 No protein-ligand interaction detected (PLIP) 7Q9.132: 5 residues within 4Å: Ligands: 17F.36, 7Q9.113, 7Q9.133, 7Q9.136, 7Q9.155 No protein-ligand interaction detected (PLIP) 7Q9.133: 4 residues within 4Å: Ligands: 7Q9.85, 7Q9.132, 7Q9.155, 17F.158 No protein-ligand interaction detected (PLIP) 7Q9.134: 5 residues within 4Å: Ligands: 7Q9.50, 17F.114, 7Q9.137, 7Q9.138, 7Q9.148 No protein-ligand interaction detected (PLIP) 7Q9.135: 5 residues within 4Å: Ligands: 7Q9.112, 7Q9.120, 7Q9.126, 7Q9.149, 7Q9.153 No protein-ligand interaction detected (PLIP) 7Q9.136: 5 residues within 4Å: Chain D: F.188 Ligands: 7Q9.37, 17F.70, 7Q9.132, 17F.156 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.188, D:F.188 7Q9.137: 6 residues within 4Å: Chain D: L.100 Ligands: 7Q9.86, 17F.114, 7Q9.118, 7Q9.134, 7Q9.148 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.100 7Q9.138: 7 residues within 4Å: Ligands: 7Q9.49, 17F.105, 7Q9.115, 7Q9.122, 7Q9.134, 7Q9.144, 7Q9.164 No protein-ligand interaction detected (PLIP) 7Q9.139: 2 residues within 4Å: Ligands: 7Q9.117, 7Q9.163 No protein-ligand interaction detected (PLIP) 7Q9.140: 3 residues within 4Å: Chain D: R.75 Ligands: 7Q9.122, 7Q9.144 No protein-ligand interaction detected (PLIP) 7Q9.143: 6 residues within 4Å: Ligands: 7Q9.60, 7Q9.72, 7Q9.119, 17F.124, 17F.141, 17F.160 No protein-ligand interaction detected (PLIP) 7Q9.144: 8 residues within 4Å: Chain D: V.78, E.79, R.82, Q.86, R.90 Ligands: 7Q9.138, 7Q9.140, 7Q9.164 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.78, D:R.82, D:Q.86 Salt bridges: D:R.90, D:R.90 7Q9.145: 2 residues within 4Å: Ligands: 7Q9.129, 7Q9.150 No protein-ligand interaction detected (PLIP) 7Q9.146: 5 residues within 4Å: Chain D: Q.64, W.67, Q.68 Ligands: 7Q9.123, 7Q9.152 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Q.64, D:W.67 7Q9.147: 6 residues within 4Å: Chain D: L.49, E.50, K.53 Ligands: 7Q9.66, 7Q9.128, 7Q9.162 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.49 7Q9.148: 7 residues within 4Å: Chain D: L.93, L.96, Q.97 Ligands: 17F.65, 7Q9.134, 7Q9.137, 7Q9.164 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.93, D:L.96, D:L.96, D:Q.97 7Q9.149: 8 residues within 4Å: Chain D: L.148, Y.151, H.152 Ligands: 17F.71, 7Q9.126, 7Q9.135, 7Q9.153, 7Q9.159 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.148, D:L.148, D:Y.151, D:Y.151, D:H.152 7Q9.150: 5 residues within 4Å: Ligands: 7Q9.56, 7Q9.129, 7Q9.130, 7Q9.145, 7Q9.163 No protein-ligand interaction detected (PLIP) 7Q9.151: 6 residues within 4Å: Chain D: K.167, L.170 Ligands: 7Q9.81, 17F.83, 7Q9.131, 7Q9.157 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.167, D:L.170 7Q9.152: 7 residues within 4Å: Chain D: L.60, D.61, Q.64 Ligands: 7Q9.123, 17F.127, 7Q9.146, 7Q9.162 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.60, D:D.61 7Q9.153: 6 residues within 4Å: Chain D: L.137, K.141 Ligands: 7Q9.120, 7Q9.135, 17F.141, 7Q9.149 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.137 Salt bridges: D:K.141, D:K.141 7Q9.154: 6 residues within 4Å: Chain D: L.162, S.163, A.166 Ligands: 7Q9.125, 7Q9.126, 7Q9.159 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.166 7Q9.155: 7 residues within 4Å: Chain D: L.199 Ligands: 7Q9.80, 7Q9.82, 7Q9.132, 7Q9.133, 17F.158, 7Q9.161 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.199 7Q9.157: 5 residues within 4Å: Chain D: R.174 Ligands: 7Q9.11, 7Q9.74, 7Q9.151, 17F.156 No protein-ligand interaction detected (PLIP) 7Q9.159: 5 residues within 4Å: Chain D: L.159, L.162 Ligands: 7Q9.126, 7Q9.149, 7Q9.154 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.162 7Q9.161: 9 residues within 4Å: Chain C: L.181 Chain D: F.188, L.192, E.193, Y.195, T.196 Ligands: 7Q9.80, 7Q9.155, 17F.156 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.188, D:L.192, D:L.192, D:Y.195, D:Y.195, D:Y.195, D:T.196, C:L.181 7Q9.162: 10 residues within 4Å: Chain C: L.129 Chain D: K.53, Q.57, L.60 Ligands: 7Q9.57, 7Q9.123, 17F.127, 7Q9.128, 7Q9.147, 7Q9.152 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.53, D:L.60, C:L.129 7Q9.163: 6 residues within 4Å: Chain C: Y.151 Chain D: Q.28 Ligands: 7Q9.77, 7Q9.130, 7Q9.139, 7Q9.150 No protein-ligand interaction detected (PLIP) 7Q9.164: 10 residues within 4Å: Chain C: K.92 Chain D: Q.86, A.89, R.90, K.92, L.93 Ligands: 17F.65, 7Q9.138, 7Q9.144, 7Q9.148 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:K.92, D:A.89, D:R.90, D:R.90, D:K.92, D:L.93, D:L.93, D:L.93 Salt bridges: D:R.90

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

17F.8: 9 residues within 4Å: Chain B: T.183 Ligands: 7Q9.4, 7Q9.9, 7Q9.11, 7Q9.13, 7Q9.90, 17F.97, 7Q9.108, 7Q9.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.183 17F.14: 5 residues within 4Å: Chain A: K.176 Ligands: 7Q9.9, 7Q9.12, 7Q9.76, 7Q9.126 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.176 17F.25: 12 residues within 4Å: Chain B: K.177, K.178, K.180, S.181, K.182 Ligands: 7Q9.4, 7Q9.20, 7Q9.23, 7Q9.29, 17F.31, 7Q9.34, 7Q9.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.182 Salt bridges: B:K.177, B:K.178, B:K.178, B:K.178 17F.31: 8 residues within 4Å: Chain B: K.182, K.184 Ligands: 7Q9.11, 17F.25, 7Q9.34, 17F.36, 7Q9.37, 7Q9.113 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.182, B:K.182, B:K.184 17F.32: 6 residues within 4Å: Ligands: 7Q9.28, 7Q9.33, 7Q9.43, 7Q9.52, 17F.95, 7Q9.107 No protein-ligand interaction detected (PLIP) 17F.36: 7 residues within 4Å: Ligands: 17F.31, 7Q9.34, 7Q9.37, 7Q9.59, 7Q9.80, 7Q9.82, 7Q9.132 No protein-ligand interaction detected (PLIP) 17F.38: 6 residues within 4Å: Ligands: 7Q9.24, 7Q9.28, 7Q9.45, 7Q9.46, 17F.93, 17F.95 No protein-ligand interaction detected (PLIP) 17F.47: 6 residues within 4Å: Ligands: 17F.48, 17F.53, 7Q9.61, 17F.64, 7Q9.118, 17F.142 No protein-ligand interaction detected (PLIP) 17F.48: 7 residues within 4Å: Ligands: 7Q9.40, 7Q9.42, 17F.47, 7Q9.50, 7Q9.61, 7Q9.63, 17F.114 No protein-ligand interaction detected (PLIP) 17F.53: 5 residues within 4Å: Ligands: 7Q9.41, 7Q9.44, 17F.47, 17F.64, 7Q9.118 No protein-ligand interaction detected (PLIP) 17F.54: 8 residues within 4Å: Ligands: 7Q9.43, 7Q9.52, 7Q9.57, 7Q9.66, 7Q9.75, 7Q9.78, 17F.127, 7Q9.128 No protein-ligand interaction detected (PLIP) 17F.64: 9 residues within 4Å: Chain C: Q.64, K.65, Q.68, M.71 Ligands: 17F.47, 17F.53, 7Q9.72, 17F.124, 17F.160 No protein-ligand interaction detected (PLIP) 17F.65: 7 residues within 4Å: Chain C: Q.86 Ligands: 7Q9.49, 7Q9.50, 7Q9.69, 7Q9.115, 7Q9.148, 7Q9.164 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.86 17F.70: 6 residues within 4Å: Chain C: F.188, L.189 Ligands: 7Q9.37, 7Q9.55, 7Q9.80, 7Q9.136 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.188, C:F.188, C:F.188, C:L.189 17F.71: 8 residues within 4Å: Chain C: Q.28, W.31, D.32, E.35 Ligands: 7Q9.15, 7Q9.73, 7Q9.76, 7Q9.149 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.28, C:W.31, C:D.32, C:E.35 17F.83: 6 residues within 4Å: Chain C: L.199, N.200 Ligands: 7Q9.17, 7Q9.74, 7Q9.81, 7Q9.151 No protein-ligand interaction detected (PLIP) 17F.87: 6 residues within 4Å: Ligands: 7Q9.20, 7Q9.21, 7Q9.24, 7Q9.88, 7Q9.89, 7Q9.90 No protein-ligand interaction detected (PLIP) 17F.91: 4 residues within 4Å: Ligands: 7Q9.23, 7Q9.96, 7Q9.98, 7Q9.102 No protein-ligand interaction detected (PLIP) 17F.93: 7 residues within 4Å: Ligands: 17F.38, 7Q9.88, 7Q9.89, 17F.95, 7Q9.99, 17F.104, 17F.105 No protein-ligand interaction detected (PLIP) 17F.95: 8 residues within 4Å: Ligands: 7Q9.28, 17F.32, 17F.38, 7Q9.88, 17F.93, 7Q9.96, 17F.104, 7Q9.110 No protein-ligand interaction detected (PLIP) 17F.97: 8 residues within 4Å: Ligands: 7Q9.4, 7Q9.6, 17F.8, 7Q9.90, 7Q9.94, 7Q9.101, 7Q9.108, 7Q9.109 No protein-ligand interaction detected (PLIP) 17F.103: 5 residues within 4Å: Ligands: 7Q9.92, 7Q9.94, 7Q9.106, 7Q9.112, 7Q9.119 No protein-ligand interaction detected (PLIP) 17F.104: 8 residues within 4Å: Ligands: 7Q9.45, 17F.93, 17F.95, 7Q9.99, 17F.105, 7Q9.110, 7Q9.121, 7Q9.123 No protein-ligand interaction detected (PLIP) 17F.105: 9 residues within 4Å: Ligands: 7Q9.39, 7Q9.42, 17F.93, 7Q9.99, 17F.104, 7Q9.115, 7Q9.121, 7Q9.122, 7Q9.138 No protein-ligand interaction detected (PLIP) 17F.114: 6 residues within 4Å: Ligands: 17F.48, 7Q9.100, 7Q9.115, 7Q9.118, 7Q9.134, 7Q9.137 No protein-ligand interaction detected (PLIP) 17F.124: 9 residues within 4Å: Ligands: 7Q9.44, 17F.64, 7Q9.72, 7Q9.106, 7Q9.118, 7Q9.119, 17F.142, 7Q9.143, 17F.160 No protein-ligand interaction detected (PLIP) 17F.127: 7 residues within 4Å: Ligands: 7Q9.43, 17F.54, 7Q9.110, 7Q9.123, 7Q9.128, 7Q9.152, 7Q9.162 No protein-ligand interaction detected (PLIP) 17F.141: 6 residues within 4Å: Chain D: L.133, L.137, L.140 Ligands: 7Q9.120, 7Q9.143, 7Q9.153 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.133, D:L.137, D:L.137, D:L.140 17F.142: 8 residues within 4Å: Chain C: W.67 Chain D: V.115, L.118 Ligands: 17F.47, 7Q9.86, 7Q9.118, 17F.124, 17F.160 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.67, D:V.115, D:V.115, D:L.118 17F.156: 7 residues within 4Å: Chain D: L.181, F.184, K.185, F.188 Ligands: 7Q9.136, 7Q9.157, 7Q9.161 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.184, D:F.184, D:K.185, D:F.188 17F.158: 6 residues within 4Å: Chain D: S.14, F.16, S.17, R.20 Ligands: 7Q9.133, 7Q9.155 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.16 17F.160: 8 residues within 4Å: Chain D: L.118, R.119 Ligands: 17F.64, 7Q9.72, 7Q9.119, 17F.124, 17F.142, 7Q9.143 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.118, D:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.Y. et al., Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization. Chem Sci (2021)

Release Date

2021-09-22

Peptides

GTPase KRas: AB
Apolipoprotein A-I: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

GTPase KRas

Apolipoprotein A-I

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