SMTL ID : 6cc9.1

NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc

Coordinates

PDB Format

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: 8 residues within 4Å: Chain A: Y.151, A.155 Chain B: T.185, C.187 Ligands: PCW.24, 17F.39, PCW.61, PCW.64 Ligand excluded by PLIP PCW.2: 4 residues within 4Å: Ligands: PCW.6, PCW.16, PCW.23, 17F.42 Ligand excluded by PLIP PCW.3: 8 residues within 4Å: Chain A: F.16, L.19 Chain B: E.5, K.7 Ligands: PCW.23, PCW.29, EWS.50, PCW.56 Ligand excluded by PLIP PCW.4: 8 residues within 4Å: Chain B: Q.72, R.75, V.105 Chain C: L.140 Ligands: PCW.15, PCW.36, PCW.76, 17F.81 Ligand excluded by PLIP PCW.5: 5 residues within 4Å: Ligands: PCW.18, PCW.20, 17F.39, PCW.59, PCW.64 Ligand excluded by PLIP PCW.6: 8 residues within 4Å: Chain A: L.199 Chain B: K.186 Ligands: PCW.2, 17F.7, PCW.11, PCW.12, 17F.38, 17F.41 Ligand excluded by PLIP PCW.8: 5 residues within 4Å: Ligands: PCW.10, PCW.11, PCW.16, PCW.60, 17F.80 Ligand excluded by PLIP PCW.9: 6 residues within 4Å: Ligands: PCW.10, 17F.38, 17F.41, PCW.63, PCW.69, 17F.80 Ligand excluded by PLIP PCW.10: 4 residues within 4Å: Ligands: PCW.8, PCW.9, PCW.11, 17F.80 Ligand excluded by PLIP PCW.11: 5 residues within 4Å: Ligands: PCW.6, PCW.8, PCW.10, PCW.60, PCW.66 Ligand excluded by PLIP PCW.12: 16 residues within 4Å: Chain B: K.184, T.185, K.186 Ligands: PCW.6, 17F.7, PCW.14, PCW.16, PCW.24, PCW.31, 17F.38, 17F.39, 17F.41, 17F.43, PCW.61, PCW.69, PCW.73 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Ligands: PCW.21, PCW.25, PCW.26, PCW.28 Ligand excluded by PLIP PCW.14: 8 residues within 4Å: Chain B: K.186 Ligands: PCW.12, PCW.20, PCW.24, 17F.39, 17F.41, 17F.43, PCW.61 Ligand excluded by PLIP PCW.15: 13 residues within 4Å: Chain B: M.172, K.177 Ligands: PCW.4, 17F.7, PCW.16, PCW.19, PCW.23, PCW.29, PCW.33, 17F.42, PCW.46, PCW.68, 17F.81 Ligand excluded by PLIP PCW.16: 9 residues within 4Å: Ligands: PCW.2, 17F.7, PCW.8, PCW.12, PCW.15, 17F.38, PCW.46, PCW.60, PCW.73 Ligand excluded by PLIP PCW.17: 11 residues within 4Å: Chain B: K.177 Ligands: PCW.19, PCW.22, PCW.29, PCW.31, PCW.33, PCW.35, 17F.37, 17F.43, PCW.45, PCW.46 Ligand excluded by PLIP PCW.18: 7 residues within 4Å: Chain B: K.181 Ligands: PCW.5, PCW.20, PCW.27, 17F.39, 17F.40, PCW.51 Ligand excluded by PLIP PCW.19: 13 residues within 4Å: Chain B: D.107, K.177 Ligands: PCW.15, PCW.17, PCW.22, PCW.29, PCW.30, PCW.33, 17F.37, 17F.42, PCW.45, 17F.47, PCW.67 Ligand excluded by PLIP PCW.20: 13 residues within 4Å: Chain B: K.179, K.180, K.181 Ligands: PCW.5, PCW.14, PCW.18, PCW.27, PCW.35, 17F.39, 17F.40, 17F.43, PCW.54, PCW.59 Ligand excluded by PLIP PCW.21: 7 residues within 4Å: Chain B: K.179 Ligands: PCW.13, PCW.25, PCW.28, PCW.32, 17F.37, 17F.40 Ligand excluded by PLIP PCW.22: 11 residues within 4Å: Chain B: K.178 Ligands: PCW.17, PCW.19, PCW.26, PCW.28, PCW.30, PCW.35, 17F.37, 17F.40, 17F.47, PCW.57 Ligand excluded by PLIP PCW.23: 6 residues within 4Å: Chain B: K.169 Ligands: PCW.2, PCW.3, PCW.15, PCW.29, 17F.42 Ligand excluded by PLIP PCW.24: 9 residues within 4Å: Chain B: K.186, C.187 Ligands: PCW.1, PCW.12, PCW.14, 17F.39, 17F.41, 17F.43, PCW.61 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Ligands: PCW.13, PCW.21, PCW.28, 17F.40, PCW.57, PCW.65, 17F.77, 17F.82, 17F.83 Ligand excluded by PLIP PCW.26: 8 residues within 4Å: Chain B: K.178 Ligands: PCW.13, PCW.22, PCW.28, PCW.30, PCW.34, PCW.58, 17F.82 Ligand excluded by PLIP PCW.27: 8 residues within 4Å: Chain B: K.179 Ligands: PCW.18, PCW.20, PCW.32, PCW.35, 17F.40, PCW.51, PCW.55 Ligand excluded by PLIP PCW.28: 10 residues within 4Å: Chain B: K.178 Ligands: PCW.13, PCW.21, PCW.22, PCW.25, PCW.26, PCW.30, 17F.37, PCW.65, 17F.81 Ligand excluded by PLIP PCW.29: 10 residues within 4Å: Ligands: PCW.3, PCW.15, PCW.17, PCW.19, PCW.23, PCW.30, PCW.36, 17F.42, PCW.45, PCW.67 Ligand excluded by PLIP PCW.30: 11 residues within 4Å: Ligands: PCW.19, PCW.22, PCW.26, PCW.28, PCW.29, PCW.34, PCW.36, PCW.71, PCW.72, PCW.76, 17F.81 Ligand excluded by PLIP PCW.31: 9 residues within 4Å: Chain B: K.177, K.180 Ligands: 17F.7, PCW.12, PCW.17, PCW.33, 17F.43, PCW.44, PCW.46 Ligand excluded by PLIP PCW.32: 6 residues within 4Å: Chain B: K.179 Ligands: PCW.21, PCW.27, 17F.40, PCW.51, 17F.77 Ligand excluded by PLIP PCW.33: 7 residues within 4Å: Ligands: PCW.15, PCW.17, PCW.19, PCW.31, PCW.45, PCW.46, PCW.72 Ligand excluded by PLIP PCW.34: 4 residues within 4Å: Ligands: PCW.26, PCW.30, PCW.72, 17F.81 Ligand excluded by PLIP PCW.35: 10 residues within 4Å: Chain B: K.179, K.180 Ligands: PCW.17, PCW.20, PCW.22, PCW.27, 17F.37, 17F.40, 17F.43, PCW.54 Ligand excluded by PLIP PCW.36: 6 residues within 4Å: Chain B: D.107 Ligands: PCW.4, PCW.29, PCW.30, PCW.58, PCW.76 Ligand excluded by PLIP PCW.44: 7 residues within 4Å: Ligands: PCW.31, 17F.43, 17F.47, PCW.52, PCW.53, PCW.73, PCW.75 Ligand excluded by PLIP PCW.45: 7 residues within 4Å: Ligands: PCW.17, PCW.19, PCW.29, PCW.33, PCW.52, PCW.67, PCW.72 Ligand excluded by PLIP PCW.46: 9 residues within 4Å: Ligands: PCW.15, PCW.16, PCW.17, PCW.31, PCW.33, PCW.52, PCW.60, PCW.72, PCW.73 Ligand excluded by PLIP PCW.51: 5 residues within 4Å: Ligands: PCW.18, PCW.27, PCW.32, PCW.54, 17F.77 Ligand excluded by PLIP PCW.52: 4 residues within 4Å: Ligands: PCW.44, PCW.45, PCW.46, 17F.47 Ligand excluded by PLIP PCW.53: 8 residues within 4Å: Ligands: 17F.37, PCW.44, 17F.47, PCW.55, PCW.57, PCW.75, 17F.78, 17F.82 Ligand excluded by PLIP PCW.54: 6 residues within 4Å: Ligands: PCW.20, PCW.35, PCW.51, PCW.55, PCW.75, 17F.77 Ligand excluded by PLIP PCW.55: 7 residues within 4Å: Ligands: PCW.27, PCW.53, PCW.54, PCW.57, PCW.65, 17F.77, 17F.79 Ligand excluded by PLIP PCW.56: 3 residues within 4Å: Ligands: PCW.3, PCW.62, PCW.67 Ligand excluded by PLIP PCW.57: 8 residues within 4Å: Ligands: PCW.22, PCW.25, 17F.37, PCW.53, PCW.55, PCW.65, 17F.82, 17F.83 Ligand excluded by PLIP PCW.58: 3 residues within 4Å: Ligands: PCW.26, PCW.36, 17F.81 Ligand excluded by PLIP PCW.59: 6 residues within 4Å: Ligands: PCW.5, PCW.20, 17F.39, PCW.64, PCW.74, PCW.75 Ligand excluded by PLIP PCW.60: 6 residues within 4Å: Ligands: PCW.8, PCW.11, PCW.16, PCW.46, PCW.66, PCW.67 Ligand excluded by PLIP PCW.61: 11 residues within 4Å: Ligands: PCW.1, PCW.12, PCW.14, PCW.24, 17F.39, 17F.41, PCW.63, PCW.64, PCW.69, PCW.73, PCW.74 Ligand excluded by PLIP PCW.62: 4 residues within 4Å: Ligands: PCW.56, PCW.67, PCW.68, PCW.76 Ligand excluded by PLIP PCW.63: 6 residues within 4Å: Ligands: PCW.9, 17F.38, 17F.41, PCW.61, PCW.69, PCW.73 Ligand excluded by PLIP PCW.64: 5 residues within 4Å: Ligands: PCW.1, PCW.5, PCW.59, PCW.61, PCW.69 Ligand excluded by PLIP PCW.65: 9 residues within 4Å: Ligands: PCW.25, PCW.28, 17F.40, PCW.55, PCW.57, 17F.77, 17F.79, 17F.82, 17F.83 Ligand excluded by PLIP PCW.66: 3 residues within 4Å: Ligands: PCW.11, PCW.60, PCW.67 Ligand excluded by PLIP PCW.67: 9 residues within 4Å: Ligands: PCW.19, PCW.29, PCW.45, PCW.56, PCW.60, PCW.62, PCW.66, PCW.68, PCW.76 Ligand excluded by PLIP PCW.68: 7 residues within 4Å: Ligands: PCW.15, 17F.42, PCW.62, PCW.67, PCW.72, PCW.76, 17F.81 Ligand excluded by PLIP PCW.69: 7 residues within 4Å: Ligands: PCW.9, PCW.12, 17F.38, 17F.41, PCW.61, PCW.63, PCW.64 Ligand excluded by PLIP PCW.70: 4 residues within 4Å: Chain C: A.89, K.92 Ligands: PCW.71, 17F.83 Ligand excluded by PLIP PCW.71: 6 residues within 4Å: Ligands: PCW.30, 17F.37, PCW.70, PCW.72, 17F.81, 17F.82 Ligand excluded by PLIP PCW.72: 10 residues within 4Å: Ligands: PCW.30, PCW.33, PCW.34, 17F.37, PCW.45, PCW.46, 17F.47, PCW.68, PCW.71, 17F.78 Ligand excluded by PLIP PCW.73: 9 residues within 4Å: Ligands: 17F.7, PCW.12, PCW.16, 17F.38, 17F.43, PCW.44, PCW.46, PCW.61, PCW.63 Ligand excluded by PLIP PCW.74: 5 residues within 4Å: Ligands: 17F.39, 17F.43, PCW.59, PCW.61, PCW.75 Ligand excluded by PLIP PCW.75: 5 residues within 4Å: Ligands: PCW.44, PCW.53, PCW.54, PCW.59, PCW.74 Ligand excluded by PLIP PCW.76: 7 residues within 4Å: Ligands: PCW.4, PCW.30, PCW.36, PCW.62, PCW.67, PCW.68, 17F.81 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.7: 7 residues within 4Å: Ligands: PCW.6, PCW.12, PCW.15, PCW.16, PCW.31, 17F.38, PCW.73 No protein-ligand interaction detected (PLIP) 17F.37: 16 residues within 4Å: Chain B: K.178, K.179 Ligands: PCW.17, PCW.19, PCW.21, PCW.22, PCW.28, PCW.35, 17F.40, 17F.43, 17F.47, PCW.53, PCW.57, PCW.71, PCW.72, 17F.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.179 Salt bridges: B:K.178 17F.38: 11 residues within 4Å: Chain B: K.184, K.186 Ligands: PCW.6, 17F.7, PCW.9, PCW.12, PCW.16, 17F.41, PCW.63, PCW.69, PCW.73 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.186, B:K.186, B:K.186 17F.39: 12 residues within 4Å: Chain B: K.181 Ligands: PCW.1, PCW.5, PCW.12, PCW.14, PCW.18, PCW.20, PCW.24, 17F.43, PCW.59, PCW.61, PCW.74 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.181 17F.40: 12 residues within 4Å: Chain B: K.179 Ligands: PCW.18, PCW.20, PCW.21, PCW.22, PCW.25, PCW.27, PCW.32, PCW.35, 17F.37, PCW.65, 17F.77 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.179 17F.41: 10 residues within 4Å: Chain B: K.186 Ligands: PCW.6, PCW.9, PCW.12, PCW.14, PCW.24, 17F.38, PCW.61, PCW.63, PCW.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.186 Salt bridges: B:K.186 17F.42: 7 residues within 4Å: Chain B: K.106 Ligands: PCW.2, PCW.15, PCW.19, PCW.23, PCW.29, PCW.68 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.106 17F.43: 15 residues within 4Å: Chain B: K.180, S.183, K.184 Ligands: PCW.12, PCW.14, PCW.17, PCW.20, PCW.24, PCW.31, PCW.35, 17F.37, 17F.39, PCW.44, PCW.73, PCW.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.180 Salt bridges: B:K.180 17F.47: 8 residues within 4Å: Ligands: PCW.19, PCW.22, 17F.37, PCW.44, PCW.52, PCW.53, PCW.72, 17F.78 No protein-ligand interaction detected (PLIP) 17F.77: 8 residues within 4Å: Ligands: PCW.25, PCW.32, 17F.40, PCW.51, PCW.54, PCW.55, PCW.65, 17F.79 No protein-ligand interaction detected (PLIP) 17F.78: 5 residues within 4Å: Ligands: 17F.37, 17F.47, PCW.53, PCW.72, 17F.82 No protein-ligand interaction detected (PLIP) 17F.79: 5 residues within 4Å: Chain C: V.78 Ligands: PCW.55, PCW.65, 17F.77, 17F.83 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.78 17F.80: 4 residues within 4Å: Chain C: L.199 Ligands: PCW.8, PCW.9, PCW.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.199 17F.81: 9 residues within 4Å: Ligands: PCW.4, PCW.15, PCW.28, PCW.30, PCW.34, PCW.58, PCW.68, PCW.71, PCW.76 No protein-ligand interaction detected (PLIP) 17F.82: 7 residues within 4Å: Ligands: PCW.25, PCW.26, PCW.53, PCW.57, PCW.65, PCW.71, 17F.78 No protein-ligand interaction detected (PLIP) 17F.83: 5 residues within 4Å: Ligands: PCW.25, PCW.57, PCW.65, PCW.70, 17F.79 No protein-ligand interaction detected (PLIP)

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

GNP.48: 21 residues within 4Å: Chain B: 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, N.118, K.119, D.121, L.122, S.147, A.148, K.149 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.15, B:G.17, B:K.18, B:S.19, B:S.19, B:S.19, B:V.31, B:D.32, B:K.119, B:S.147, B:A.148, B:K.149 Salt bridges: B:D.121 pi-Stacking: B:F.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.49: 4 residues within 4Å: Chain B: T.37, D.40, Y.42, D.59 1 PLIP interactions: 1 interactions with chain B Metal complexes: 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.50: 14 residues within 4Å: Chain B: K.7, L.8, V.9, V.10, V.11, D.56, I.57, L.58, T.60, M.69, Y.73, M.74, T.76 Ligands: PCW.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.9, B:V.9, B:L.58, B:L.58 Hydrogen bonds: B:L.8, B:L.58

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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