SMTL ID : 6w4f.1

NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc

Coordinates

PDB Format Compare

Method

SOLUTION NMR

Oligo State

hetero-2-2-mer

Ligands

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

PCW.1: 5 residues within 4Å: Chain C: K.183 Ligands: PCW.31, PCW.34, PCW.39, PCW.64 Ligand excluded by PLIP PCW.2: 5 residues within 4Å: Ligands: PCW.7, PCW.9, 17F.55, PCW.77, PCW.78 Ligand excluded by PLIP PCW.3: 5 residues within 4Å: Chain D: M.169 Ligands: PCW.13, 17F.14, PCW.75, PCW.76 Ligand excluded by PLIP PCW.4: 10 residues within 4Å: Chain C: K.176, K.178, K.179 Ligands: 17F.15, PCW.31, PCW.58, PCW.62, PCW.64, 17F.70, 17F.82 Ligand excluded by PLIP PCW.5: 4 residues within 4Å: Chain A: L.122 Chain B: Y.59 Ligands: PCW.21, 17F.48 Ligand excluded by PLIP PCW.6: 6 residues within 4Å: Ligands: PCW.11, PCW.26, PCW.62, PCW.65, 17F.70, 17F.71 Ligand excluded by PLIP PCW.7: 10 residues within 4Å: Ligands: PCW.2, PCW.9, PCW.35, 17F.55, PCW.62, PCW.63, PCW.68, 17F.69, 17F.71, PCW.77 Ligand excluded by PLIP PCW.8: 8 residues within 4Å: Chain A: F.16, L.19 Chain B: H.158 Chain D: K.174, K.176 Ligands: PCW.17, PCW.76, 17F.83 Ligand excluded by PLIP PCW.9: 7 residues within 4Å: Chain D: K.183 Ligands: PCW.2, PCW.7, PCW.12, PCW.77, PCW.78, PCW.80 Ligand excluded by PLIP PCW.10: 4 residues within 4Å: Chain A: L.49 Chain D: S.180, K.181 Ligands: PCW.81 Ligand excluded by PLIP PCW.11: 4 residues within 4Å: Ligands: PCW.6, PCW.18, PCW.64, 17F.70 Ligand excluded by PLIP PCW.12: 5 residues within 4Å: Chain D: K.183 Ligands: PCW.9, 17F.54, PCW.78, PCW.81 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Ligands: PCW.3, 17F.14, PCW.75, 17F.82 Ligand excluded by PLIP PCW.16: 6 residues within 4Å: Ligands: PCW.19, PCW.20, PCW.22, PCW.30, PCW.37, 17F.52 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Chain A: F.16 Ligands: PCW.8, PCW.19, PCW.32, PCW.37 Ligand excluded by PLIP PCW.18: 7 residues within 4Å: Ligands: PCW.11, PCW.23, PCW.26, PCW.34, PCW.43, PCW.45, PCW.46 Ligand excluded by PLIP PCW.19: 6 residues within 4Å: Ligands: PCW.16, PCW.17, PCW.30, PCW.36, PCW.37, PCW.38 Ligand excluded by PLIP PCW.20: 3 residues within 4Å: Ligands: PCW.16, PCW.37, 17F.52 Ligand excluded by PLIP PCW.21: 8 residues within 4Å: Chain B: F.63, E.70 Ligands: PCW.5, PCW.27, 17F.48, 17F.51, PCW.65, 17F.71 Ligand excluded by PLIP PCW.22: 6 residues within 4Å: Ligands: PCW.16, PCW.23, PCW.30, PCW.44, 17F.50, PCW.84 Ligand excluded by PLIP PCW.23: 8 residues within 4Å: Ligands: PCW.18, PCW.22, PCW.25, PCW.26, PCW.43, PCW.46, 17F.49, 17F.50 Ligand excluded by PLIP PCW.24: 7 residues within 4Å: Ligands: 17F.15, PCW.31, PCW.33, PCW.39, PCW.44, 17F.52, 17F.82 Ligand excluded by PLIP PCW.25: 6 residues within 4Å: Ligands: PCW.23, PCW.27, PCW.28, PCW.46, 17F.49, 17F.54 Ligand excluded by PLIP PCW.26: 6 residues within 4Å: Ligands: PCW.6, PCW.18, PCW.23, PCW.45, PCW.46, 17F.48 Ligand excluded by PLIP PCW.27: 6 residues within 4Å: Ligands: PCW.21, PCW.25, PCW.28, PCW.46, 17F.48, 17F.51 Ligand excluded by PLIP PCW.28: 8 residues within 4Å: Ligands: PCW.25, PCW.27, PCW.35, PCW.40, 17F.48, 17F.55, 17F.71, PCW.77 Ligand excluded by PLIP PCW.29: 2 residues within 4Å: Ligands: 17F.53, PCW.81 Ligand excluded by PLIP PCW.30: 6 residues within 4Å: Ligands: PCW.16, PCW.19, PCW.22, PCW.36, 17F.83, PCW.84 Ligand excluded by PLIP PCW.31: 7 residues within 4Å: Ligands: PCW.1, PCW.4, PCW.24, PCW.33, PCW.39, PCW.43, PCW.45 Ligand excluded by PLIP PCW.32: 3 residues within 4Å: Ligands: PCW.17, PCW.38, PCW.47 Ligand excluded by PLIP PCW.33: 6 residues within 4Å: Ligands: 17F.15, PCW.24, PCW.31, PCW.39, PCW.44, 17F.82 Ligand excluded by PLIP PCW.34: 4 residues within 4Å: Ligands: PCW.1, PCW.18, PCW.39, PCW.45 Ligand excluded by PLIP PCW.35: 6 residues within 4Å: Ligands: PCW.7, PCW.28, 17F.55, PCW.63, 17F.71, PCW.77 Ligand excluded by PLIP PCW.36: 9 residues within 4Å: Ligands: PCW.19, PCW.30, PCW.37, PCW.38, PCW.47, PCW.59, PCW.61, PCW.76, PCW.84 Ligand excluded by PLIP PCW.37: 5 residues within 4Å: Ligands: PCW.16, PCW.17, PCW.19, PCW.20, PCW.36 Ligand excluded by PLIP PCW.38: 10 residues within 4Å: Ligands: PCW.19, PCW.32, PCW.36, PCW.42, PCW.47, 17F.53, PCW.59, PCW.61, PCW.76, PCW.79 Ligand excluded by PLIP PCW.39: 6 residues within 4Å: Chain B: F.16 Ligands: PCW.1, PCW.24, PCW.31, PCW.33, PCW.34 Ligand excluded by PLIP PCW.40: 3 residues within 4Å: Ligands: PCW.28, PCW.41, 17F.55 Ligand excluded by PLIP PCW.41: 5 residues within 4Å: Ligands: PCW.40, PCW.42, 17F.53, 17F.54, 17F.55 Ligand excluded by PLIP PCW.42: 10 residues within 4Å: Ligands: PCW.38, PCW.41, PCW.44, PCW.47, 17F.49, 17F.50, 17F.53, 17F.54, PCW.61, PCW.84 Ligand excluded by PLIP PCW.43: 7 residues within 4Å: Ligands: PCW.18, PCW.23, PCW.31, PCW.44, PCW.45, PCW.58, PCW.66 Ligand excluded by PLIP PCW.44: 6 residues within 4Å: Ligands: PCW.22, PCW.24, PCW.33, PCW.42, PCW.43, 17F.82 Ligand excluded by PLIP PCW.45: 6 residues within 4Å: Ligands: PCW.18, PCW.26, PCW.31, PCW.34, PCW.43, PCW.46 Ligand excluded by PLIP PCW.46: 6 residues within 4Å: Ligands: PCW.18, PCW.23, PCW.25, PCW.26, PCW.27, PCW.45 Ligand excluded by PLIP PCW.47: 5 residues within 4Å: Ligands: PCW.32, PCW.36, PCW.38, PCW.42, 17F.53 Ligand excluded by PLIP PCW.58: 8 residues within 4Å: Chain C: K.174, K.176, K.179 Ligands: PCW.4, 17F.15, PCW.43, PCW.66, 17F.82 Ligand excluded by PLIP PCW.59: 12 residues within 4Å: Ligands: 17F.14, PCW.36, PCW.38, PCW.60, PCW.61, PCW.67, PCW.75, PCW.76, PCW.79, PCW.80, 17F.83, PCW.84 Ligand excluded by PLIP PCW.60: 8 residues within 4Å: Ligands: 17F.50, PCW.59, PCW.61, PCW.63, PCW.66, PCW.67, 17F.69, PCW.80 Ligand excluded by PLIP PCW.61: 12 residues within 4Å: Ligands: PCW.36, PCW.38, PCW.42, 17F.50, PCW.59, PCW.60, PCW.67, 17F.69, PCW.76, PCW.79, PCW.81, PCW.84 Ligand excluded by PLIP PCW.62: 8 residues within 4Å: Ligands: PCW.4, PCW.6, PCW.7, PCW.65, PCW.68, 17F.70, 17F.71, 17F.72 Ligand excluded by PLIP PCW.63: 7 residues within 4Å: Ligands: PCW.7, PCW.35, PCW.60, 17F.69, 17F.71, PCW.77, PCW.80 Ligand excluded by PLIP PCW.64: 5 residues within 4Å: Chain C: K.178 Ligands: PCW.1, PCW.4, PCW.11, 17F.70 Ligand excluded by PLIP PCW.65: 5 residues within 4Å: Ligands: PCW.6, PCW.21, PCW.62, PCW.68, 17F.71 Ligand excluded by PLIP PCW.66: 6 residues within 4Å: Ligands: PCW.43, PCW.58, PCW.60, PCW.67, 17F.70, 17F.72 Ligand excluded by PLIP PCW.67: 8 residues within 4Å: Ligands: 17F.14, 17F.49, PCW.59, PCW.60, PCW.61, PCW.66, 17F.82, PCW.84 Ligand excluded by PLIP PCW.68: 6 residues within 4Å: Ligands: PCW.7, PCW.62, PCW.65, 17F.69, 17F.70, 17F.72 Ligand excluded by PLIP PCW.75: 8 residues within 4Å: Chain C: E.167 Chain D: S.170 Ligands: PCW.3, PCW.13, 17F.14, PCW.59, PCW.76, 17F.83 Ligand excluded by PLIP PCW.76: 10 residues within 4Å: Chain D: S.170 Ligands: PCW.3, PCW.8, PCW.36, PCW.38, PCW.59, PCW.61, PCW.75, PCW.79, 17F.83 Ligand excluded by PLIP PCW.77: 10 residues within 4Å: Ligands: PCW.2, PCW.7, PCW.9, PCW.28, PCW.35, 17F.48, 17F.55, PCW.63, 17F.69, PCW.78 Ligand excluded by PLIP PCW.78: 6 residues within 4Å: Ligands: PCW.2, PCW.9, PCW.12, 17F.54, PCW.77, PCW.80 Ligand excluded by PLIP PCW.79: 10 residues within 4Å: Chain D: K.178, K.179 Ligands: PCW.38, 17F.53, PCW.59, PCW.61, PCW.76, PCW.80, PCW.81, 17F.83 Ligand excluded by PLIP PCW.80: 7 residues within 4Å: Ligands: PCW.9, PCW.59, PCW.60, PCW.63, PCW.78, PCW.79, PCW.81 Ligand excluded by PLIP PCW.81: 10 residues within 4Å: Chain D: K.181, T.182, K.183 Ligands: PCW.10, PCW.12, PCW.29, 17F.53, PCW.61, PCW.79, PCW.80 Ligand excluded by PLIP PCW.84: 8 residues within 4Å: Ligands: PCW.22, PCW.30, PCW.36, PCW.42, 17F.50, PCW.59, PCW.61, PCW.67 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.14: 6 residues within 4Å: Ligands: PCW.3, PCW.13, PCW.59, PCW.67, PCW.75, 17F.82 No protein-ligand interaction detected (PLIP) 17F.15: 8 residues within 4Å: Chain C: K.175, K.177, K.179, K.181 Ligands: PCW.4, PCW.24, PCW.33, PCW.58 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.177 Salt bridges: C:K.175, C:K.177, C:K.177, C:K.177 17F.48: 8 residues within 4Å: Ligands: PCW.5, PCW.21, PCW.26, PCW.27, PCW.28, 17F.51, 17F.71, PCW.77 No protein-ligand interaction detected (PLIP) 17F.49: 6 residues within 4Å: Ligands: PCW.23, PCW.25, PCW.42, 17F.50, 17F.54, PCW.67 No protein-ligand interaction detected (PLIP) 17F.50: 9 residues within 4Å: Ligands: PCW.22, PCW.23, PCW.42, 17F.49, 17F.54, PCW.60, PCW.61, 17F.69, PCW.84 No protein-ligand interaction detected (PLIP) 17F.51: 5 residues within 4Å: Chain B: W.67, M.71 Ligands: PCW.21, PCW.27, 17F.48 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.67 17F.52: 7 residues within 4Å: Chain B: L.192, Y.195, T.196, L.199 Ligands: PCW.16, PCW.20, PCW.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.192, B:Y.195 17F.53: 7 residues within 4Å: Ligands: PCW.29, PCW.38, PCW.41, PCW.42, PCW.47, PCW.79, PCW.81 No protein-ligand interaction detected (PLIP) 17F.54: 8 residues within 4Å: Ligands: PCW.12, PCW.25, PCW.41, PCW.42, 17F.49, 17F.50, 17F.55, PCW.78 No protein-ligand interaction detected (PLIP) 17F.55: 8 residues within 4Å: Ligands: PCW.2, PCW.7, PCW.28, PCW.35, PCW.40, PCW.41, 17F.54, PCW.77 No protein-ligand interaction detected (PLIP) 17F.69: 8 residues within 4Å: Ligands: PCW.7, 17F.50, PCW.60, PCW.61, PCW.63, PCW.68, 17F.72, PCW.77 No protein-ligand interaction detected (PLIP) 17F.70: 8 residues within 4Å: Ligands: PCW.4, PCW.6, PCW.11, PCW.62, PCW.64, PCW.66, PCW.68, 17F.72 No protein-ligand interaction detected (PLIP) 17F.71: 9 residues within 4Å: Ligands: PCW.6, PCW.7, PCW.21, PCW.28, PCW.35, 17F.48, PCW.62, PCW.63, PCW.65 No protein-ligand interaction detected (PLIP) 17F.72: 5 residues within 4Å: Ligands: PCW.62, PCW.66, PCW.68, 17F.69, 17F.70 No protein-ligand interaction detected (PLIP) 17F.82: 9 residues within 4Å: Chain C: K.171 Ligands: PCW.4, PCW.13, 17F.14, PCW.24, PCW.33, PCW.44, PCW.58, PCW.67 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.171 17F.83: 9 residues within 4Å: Chain D: K.171, K.174, K.178 Ligands: PCW.8, PCW.30, PCW.59, PCW.75, PCW.76, PCW.79 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.171, D:K.178

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

GDP.56: 19 residues within 4Å: Chain C: D.11, G.12, V.13, G.14, K.15, S.16, A.17, F.27, V.28, Y.31, D.32, N.115, K.116, D.118, L.119, S.144, A.145, K.146 Ligands: MG.57 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:D.11, C:D.11, C:G.12, C:V.13, C:G.14, C:K.15, C:S.16, C:A.17, C:D.32, C:N.115, C:K.116, C:K.116, C:A.145, C:K.146 Salt bridges: C:K.15, C:D.118 pi-Stacking: C:F.27, C:F.27 GDP.73: 19 residues within 4Å: Chain D: A.10, G.12, V.13, G.14, K.15, S.16, A.17, F.27, V.28, D.32, D.56, N.115, K.116, D.118, L.119, S.144, A.145, K.146 Ligands: MG.74 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.12, D:V.13, D:G.14, D:K.15, D:S.16, D:S.16, D:A.17, D:D.32, D:N.115, D:K.116, D:K.116, D:A.145, D:K.146 Salt bridges: D:K.15, D:D.118 pi-Stacking: D:F.27, D:F.27

2 x MG: MAGNESIUM ION(Non-covalent)

MG.57: 7 residues within 4Å: Chain C: D.11, K.15, S.16, D.32, P.33, D.56 Ligands: GDP.56 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.16, C:D.32 MG.74: 5 residues within 4Å: Chain D: K.15, S.16, D.56, T.57 Ligands: GDP.73 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.16, D:D.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.Y. et al., Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-04-29

Peptides

Apolipoprotein A-I: AB
GTPase KRas: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Apolipoprotein A-I

GTPase KRas

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