SMTL ID : 6cch.1

NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)

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)(Covalent)

PCW.1: 9 residues within 4Å: Ligands: PCW.2, PCW.5, PCW.26, 17F.35, 17F.36, 17F.38, 17F.40, PCW.53, PCW.68 Ligand excluded by PLIP PCW.2: 8 residues within 4Å: Chain C: L.19 Ligands: PCW.1, PCW.5, PCW.17, PCW.53, PCW.56, PCW.64, PCW.68 Ligand excluded by PLIP PCW.3: 8 residues within 4Å: Chain B: F.92, K.130, Q.131, D.134, L.135 Ligands: PCW.18, PCW.19, PCW.23 Ligand excluded by PLIP PCW.4: 3 residues within 4Å: Ligands: PCW.7, 17F.39, PCW.61 Ligand excluded by PLIP PCW.5: 6 residues within 4Å: Ligands: PCW.1, PCW.2, PCW.17, 17F.36, 17F.38, PCW.64 Ligand excluded by PLIP PCW.6: 11 residues within 4Å: Chain B: D.107 Ligands: PCW.7, PCW.11, PCW.16, PCW.24, PCW.26, PCW.28, PCW.31, 17F.33, 17F.39, PCW.52 Ligand excluded by PLIP PCW.7: 6 residues within 4Å: Ligands: PCW.4, PCW.6, 17F.33, 17F.35, PCW.41, PCW.52 Ligand excluded by PLIP PCW.8: 4 residues within 4Å: Chain A: L.118 Chain C: Y.59, F.63 Ligands: PCW.27 Ligand excluded by PLIP PCW.9: 12 residues within 4Å: Chain B: E.109 Ligands: PCW.11, PCW.14, PCW.23, PCW.25, PCW.26, PCW.28, PCW.29, 17F.34, 17F.40, PCW.63, PCW.69 Ligand excluded by PLIP PCW.10: 3 residues within 4Å: Ligands: PCW.12, PCW.21, PCW.22 Ligand excluded by PLIP PCW.11: 13 residues within 4Å: Chain B: K.103, R.104, E.109 Ligands: PCW.6, PCW.9, PCW.16, PCW.25, PCW.28, 17F.34, PCW.63, PCW.67, 17F.74, 17F.75 Ligand excluded by PLIP PCW.12: 8 residues within 4Å: Ligands: PCW.10, PCW.21, PCW.22, PCW.30, 17F.36, 17F.37, 17F.40, PCW.51 Ligand excluded by PLIP PCW.13: 9 residues within 4Å: Ligands: PCW.14, PCW.18, PCW.23, PCW.27, 17F.34, 17F.37, PCW.47, PCW.49, PCW.57 Ligand excluded by PLIP PCW.14: 10 residues within 4Å: Chain B: R.99, K.103, S.138, Y.139 Ligands: PCW.9, PCW.13, PCW.30, 17F.34, 17F.37, 17F.75 Ligand excluded by PLIP PCW.15: 3 residues within 4Å: Chain A: F.16, L.19 Ligands: PCW.24 Ligand excluded by PLIP PCW.16: 4 residues within 4Å: Ligands: PCW.6, PCW.11, PCW.24, 17F.39 Ligand excluded by PLIP PCW.17: 6 residues within 4Å: Ligands: PCW.2, PCW.5, PCW.21, 17F.36, 17F.38, PCW.53 Ligand excluded by PLIP PCW.18: 10 residues within 4Å: Chain B: K.130, D.134 Ligands: PCW.3, PCW.13, PCW.23, 17F.37, PCW.49, PCW.57, 17F.73, 17F.80 Ligand excluded by PLIP PCW.19: 9 residues within 4Å: Chain B: E.93, L.135, Y.139 Ligands: PCW.3, PCW.23, PCW.29, PCW.50, 17F.78, 17F.79 Ligand excluded by PLIP PCW.20: 4 residues within 4Å: Ligands: PCW.24, PCW.31, PCW.72, 17F.78 Ligand excluded by PLIP PCW.21: 6 residues within 4Å: Ligands: PCW.10, PCW.12, PCW.17, PCW.22, 17F.36, PCW.51 Ligand excluded by PLIP PCW.22: 8 residues within 4Å: Ligands: PCW.10, PCW.12, PCW.21, PCW.30, 17F.36, 17F.37, PCW.46, PCW.47 Ligand excluded by PLIP PCW.23: 13 residues within 4Å: Chain B: D.134, L.135, R.137, S.138 Ligands: PCW.3, PCW.9, PCW.13, PCW.18, PCW.19, 17F.34, 17F.37, PCW.57, 17F.79 Ligand excluded by PLIP PCW.24: 9 residues within 4Å: Chain B: Y.66, R.104 Ligands: PCW.6, PCW.15, PCW.16, PCW.20, PCW.25, PCW.31, 17F.39 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Chain B: E.100 Ligands: PCW.9, PCW.11, PCW.24, PCW.29, PCW.31, PCW.66, PCW.67, PCW.72 Ligand excluded by PLIP PCW.26: 9 residues within 4Å: Ligands: PCW.1, PCW.6, PCW.9, PCW.28, 17F.33, 17F.40, PCW.43, PCW.68, PCW.69 Ligand excluded by PLIP PCW.27: 9 residues within 4Å: Chain A: M.107, H.114 Chain C: E.70 Ligands: PCW.8, PCW.13, 17F.37, PCW.47, 17F.73, 17F.76 Ligand excluded by PLIP PCW.28: 9 residues within 4Å: Ligands: PCW.6, PCW.9, PCW.11, PCW.26, PCW.42, PCW.63, PCW.67, PCW.69, 17F.75 Ligand excluded by PLIP PCW.29: 12 residues within 4Å: Chain A: D.48, V.52 Chain B: E.93 Chain C: Y.125, L.129, R.132 Ligands: PCW.9, PCW.19, PCW.25, PCW.31, PCW.66, PCW.67 Ligand excluded by PLIP PCW.30: 4 residues within 4Å: Ligands: PCW.12, PCW.14, PCW.22, 17F.40 Ligand excluded by PLIP PCW.31: 6 residues within 4Å: Ligands: PCW.6, PCW.20, PCW.24, PCW.25, PCW.29, 17F.78 Ligand excluded by PLIP PCW.32: 7 residues within 4Å: Chain A: L.199 Ligands: 17F.33, 17F.35, 17F.38, PCW.44, PCW.59, PCW.61 Ligand excluded by PLIP PCW.41: 5 residues within 4Å: Ligands: PCW.7, PCW.52, PCW.59, PCW.61, 17F.77 Ligand excluded by PLIP PCW.42: 6 residues within 4Å: Ligands: PCW.28, PCW.43, PCW.52, PCW.63, PCW.69, 17F.75 Ligand excluded by PLIP PCW.43: 6 residues within 4Å: Ligands: PCW.26, PCW.42, PCW.45, PCW.51, PCW.68, 17F.75 Ligand excluded by PLIP PCW.44: 8 residues within 4Å: Ligands: PCW.32, 17F.35, PCW.53, PCW.55, PCW.59, PCW.64, PCW.69, 17F.77 Ligand excluded by PLIP PCW.45: 6 residues within 4Å: Ligands: 17F.34, PCW.43, PCW.49, 17F.74, 17F.75, 17F.79 Ligand excluded by PLIP PCW.46: 4 residues within 4Å: Ligands: PCW.22, PCW.47, PCW.71, 17F.73 Ligand excluded by PLIP PCW.47: 8 residues within 4Å: Ligands: PCW.13, PCW.22, PCW.27, 17F.37, PCW.46, PCW.57, 17F.73, 17F.76 Ligand excluded by PLIP PCW.48: 2 residues within 4Å: Ligands: PCW.54, PCW.60 Ligand excluded by PLIP PCW.49: 8 residues within 4Å: Ligands: PCW.13, PCW.18, 17F.37, PCW.45, PCW.57, PCW.71, 17F.73, 17F.80 Ligand excluded by PLIP PCW.50: 2 residues within 4Å: Ligands: PCW.19, 17F.78 Ligand excluded by PLIP PCW.51: 7 residues within 4Å: Ligands: PCW.12, PCW.21, 17F.40, PCW.43, PCW.56, PCW.70, PCW.71 Ligand excluded by PLIP PCW.52: 8 residues within 4Å: Ligands: PCW.6, PCW.7, 17F.39, PCW.41, PCW.42, PCW.58, PCW.60, PCW.62 Ligand excluded by PLIP PCW.53: 10 residues within 4Å: Ligands: PCW.1, PCW.2, PCW.17, 17F.36, PCW.44, PCW.55, PCW.56, PCW.64, PCW.68, PCW.70 Ligand excluded by PLIP PCW.54: 2 residues within 4Å: Chain C: A.155 Ligands: PCW.48 Ligand excluded by PLIP PCW.55: 7 residues within 4Å: Ligands: 17F.35, 17F.38, PCW.44, PCW.53, PCW.64, PCW.68, PCW.69 Ligand excluded by PLIP PCW.56: 5 residues within 4Å: Ligands: PCW.2, PCW.51, PCW.53, PCW.64, PCW.70 Ligand excluded by PLIP PCW.57: 9 residues within 4Å: Ligands: PCW.13, PCW.18, PCW.23, 17F.37, PCW.47, PCW.49, 17F.76, 17F.79, 17F.80 Ligand excluded by PLIP PCW.58: 3 residues within 4Å: Chain C: L.181 Ligands: PCW.52, PCW.60 Ligand excluded by PLIP PCW.59: 5 residues within 4Å: Ligands: PCW.32, PCW.41, PCW.44, PCW.61, 17F.77 Ligand excluded by PLIP PCW.60: 6 residues within 4Å: Ligands: PCW.48, PCW.52, PCW.58, PCW.62, PCW.63, PCW.72 Ligand excluded by PLIP PCW.61: 4 residues within 4Å: Ligands: PCW.4, PCW.32, PCW.41, PCW.59 Ligand excluded by PLIP PCW.62: 4 residues within 4Å: Ligands: 17F.39, PCW.52, PCW.60, PCW.72 Ligand excluded by PLIP PCW.63: 7 residues within 4Å: Ligands: PCW.9, PCW.11, PCW.28, PCW.42, PCW.60, PCW.67, 17F.74 Ligand excluded by PLIP PCW.64: 7 residues within 4Å: Ligands: PCW.2, PCW.5, 17F.38, PCW.44, PCW.53, PCW.55, PCW.56 Ligand excluded by PLIP PCW.65: 4 residues within 4Å: Chain C: K.92, L.96, L.100 Ligands: 17F.80 Ligand excluded by PLIP PCW.66: 5 residues within 4Å: Ligands: PCW.25, PCW.29, PCW.67, 17F.78, 17F.79 Ligand excluded by PLIP PCW.67: 10 residues within 4Å: Ligands: PCW.11, PCW.25, PCW.28, PCW.29, 17F.34, PCW.63, PCW.66, PCW.69, 17F.74, 17F.75 Ligand excluded by PLIP PCW.68: 9 residues within 4Å: Ligands: PCW.1, PCW.2, PCW.26, 17F.33, PCW.43, PCW.53, PCW.55, PCW.69, PCW.70 Ligand excluded by PLIP PCW.69: 10 residues within 4Å: Ligands: PCW.9, PCW.26, PCW.28, 17F.33, 17F.35, PCW.42, PCW.44, PCW.55, PCW.67, PCW.68 Ligand excluded by PLIP PCW.70: 7 residues within 4Å: Ligands: 17F.36, 17F.40, PCW.51, PCW.53, PCW.56, PCW.68, PCW.71 Ligand excluded by PLIP PCW.71: 5 residues within 4Å: Ligands: 17F.36, PCW.46, PCW.49, PCW.51, PCW.70 Ligand excluded by PLIP PCW.72: 5 residues within 4Å: Ligands: PCW.20, PCW.25, PCW.60, 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: 8 residues within 4Å: Chain A: F.188 Ligands: PCW.6, PCW.7, PCW.26, PCW.32, 17F.35, PCW.68, PCW.69 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.188 17F.34: 12 residues within 4Å: Chain B: R.137 Ligands: PCW.9, PCW.11, PCW.13, PCW.14, PCW.23, 17F.37, 17F.40, PCW.45, PCW.67, 17F.74, 17F.75 No protein-ligand interaction detected (PLIP) 17F.35: 8 residues within 4Å: Ligands: PCW.1, PCW.7, PCW.32, 17F.33, 17F.38, PCW.44, PCW.55, PCW.69 No protein-ligand interaction detected (PLIP) 17F.36: 10 residues within 4Å: Ligands: PCW.1, PCW.5, PCW.12, PCW.17, PCW.21, PCW.22, 17F.40, PCW.53, PCW.70, PCW.71 No protein-ligand interaction detected (PLIP) 17F.37: 12 residues within 4Å: Ligands: PCW.12, PCW.13, PCW.14, PCW.18, PCW.22, PCW.23, PCW.27, 17F.34, PCW.47, PCW.49, PCW.57, 17F.73 No protein-ligand interaction detected (PLIP) 17F.38: 9 residues within 4Å: Chain A: L.173, L.177 Ligands: PCW.1, PCW.5, PCW.17, PCW.32, 17F.35, PCW.55, PCW.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.173, A:L.177, A:L.177 17F.39: 6 residues within 4Å: Ligands: PCW.4, PCW.6, PCW.16, PCW.24, PCW.52, PCW.62 No protein-ligand interaction detected (PLIP) 17F.40: 9 residues within 4Å: Ligands: PCW.1, PCW.9, PCW.12, PCW.26, PCW.30, 17F.34, 17F.36, PCW.51, PCW.70 No protein-ligand interaction detected (PLIP) 17F.73: 7 residues within 4Å: Ligands: PCW.18, PCW.27, 17F.37, PCW.46, PCW.47, PCW.49, 17F.76 No protein-ligand interaction detected (PLIP) 17F.74: 7 residues within 4Å: Ligands: PCW.11, 17F.34, PCW.45, PCW.63, PCW.67, 17F.75, 17F.79 No protein-ligand interaction detected (PLIP) 17F.75: 9 residues within 4Å: Ligands: PCW.11, PCW.14, PCW.28, 17F.34, PCW.42, PCW.43, PCW.45, PCW.67, 17F.74 No protein-ligand interaction detected (PLIP) 17F.76: 6 residues within 4Å: Chain C: V.78 Ligands: PCW.27, PCW.47, PCW.57, 17F.73, 17F.80 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.78 17F.77: 3 residues within 4Å: Ligands: PCW.41, PCW.44, PCW.59 No protein-ligand interaction detected (PLIP) 17F.78: 6 residues within 4Å: Ligands: PCW.19, PCW.20, PCW.31, PCW.50, PCW.66, PCW.72 No protein-ligand interaction detected (PLIP) 17F.79: 6 residues within 4Å: Ligands: PCW.19, PCW.23, PCW.45, PCW.57, PCW.66, 17F.74 No protein-ligand interaction detected (PLIP) 17F.80: 5 residues within 4Å: Ligands: PCW.18, PCW.49, PCW.57, PCW.65, 17F.76 No protein-ligand interaction detected (PLIP)

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

GNP.81: 24 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, T.37, G.62, N.118, K.119, D.121, L.122, S.147, A.148, K.149 Ligands: MG.82 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.15, B:K.18, B:S.19, B:V.31, B:D.32, B:D.35, B:T.37, 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.82: 5 residues within 4Å: Chain B: S.19, T.37, D.40, D.59 Ligands: GNP.81 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.37, B:D.40, B:D.59

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

2018-08-29

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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