SMTL ID : 6w4e.1

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

Coordinates

PDB Format

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 A: Y.151 Ligands: PCW.34, PCW.37, PCW.58, PCW.61 Ligand excluded by PLIP PCW.2: 5 residues within 4Å: Ligands: PCW.7, PCW.10, 17F.54, PCW.71, PCW.73 Ligand excluded by PLIP PCW.3: 5 residues within 4Å: Ligands: PCW.4, PCW.6, 17F.15, PCW.40, 17F.65 Ligand excluded by PLIP PCW.4: 7 residues within 4Å: Chain D: K.184 Ligands: PCW.3, PCW.6, 17F.15, PCW.33, PCW.40, PCW.59 Ligand excluded by PLIP PCW.5: 7 residues within 4Å: Chain A: F.16, L.19, R.20 Chain B: L.162 Ligands: PCW.11, PCW.18, 17F.65 Ligand excluded by PLIP PCW.6: 8 residues within 4Å: Ligands: PCW.3, PCW.4, PCW.11, PCW.39, PCW.41, PCW.59, 17F.65, PCW.69 Ligand excluded by PLIP PCW.7: 4 residues within 4Å: Ligands: PCW.2, PCW.10, PCW.12, PCW.71 Ligand excluded by PLIP PCW.8: 5 residues within 4Å: Ligands: PCW.11, PCW.13, PCW.41, 17F.53, PCW.75 Ligand excluded by PLIP PCW.9: 8 residues within 4Å: Chain A: L.140, R.147 Chain C: K.182, T.183, K.184 Ligands: PCW.19, PCW.60, 17F.64 Ligand excluded by PLIP PCW.10: 6 residues within 4Å: Ligands: PCW.2, PCW.7, PCW.12, 17F.22, PCW.72, PCW.73 Ligand excluded by PLIP PCW.11: 6 residues within 4Å: Ligands: PCW.5, PCW.6, PCW.8, PCW.13, PCW.59, 17F.65 Ligand excluded by PLIP PCW.12: 6 residues within 4Å: Chain A: D.48, L.49 Chain B: Y.125 Ligands: PCW.7, PCW.10, PCW.75 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Ligands: PCW.8, PCW.11, 17F.53, PCW.75 Ligand excluded by PLIP PCW.14: 2 residues within 4Å: Ligands: 17F.15, 17F.63 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Ligands: PCW.20, PCW.21, PCW.25, PCW.33, PCW.40 Ligand excluded by PLIP PCW.18: 3 residues within 4Å: Ligands: PCW.5, PCW.35, PCW.40 Ligand excluded by PLIP PCW.19: 8 residues within 4Å: Ligands: PCW.9, PCW.26, PCW.29, PCW.37, PCW.47, PCW.48, PCW.77, 17F.80 Ligand excluded by PLIP PCW.20: 5 residues within 4Å: Ligands: PCW.17, PCW.33, PCW.39, PCW.40, PCW.41 Ligand excluded by PLIP PCW.21: 3 residues within 4Å: Ligands: PCW.17, PCW.40, 17F.52 Ligand excluded by PLIP PCW.23: 8 residues within 4Å: Chain A: L.118, L.122, Y.125 Chain B: K.55, V.56, Y.59 Ligands: PCW.24, 17F.50 Ligand excluded by PLIP PCW.24: 9 residues within 4Å: Chain A: H.114 Chain B: K.66, W.67, E.70 Ligands: PCW.23, PCW.30, 17F.50, 17F.51, 17F.79 Ligand excluded by PLIP PCW.25: 6 residues within 4Å: Ligands: PCW.17, PCW.26, PCW.33, PCW.46, PCW.81, 17F.84 Ligand excluded by PLIP PCW.26: 10 residues within 4Å: Ligands: PCW.19, PCW.25, PCW.28, PCW.29, PCW.45, PCW.48, 17F.78, 17F.80, 17F.83, 17F.84 Ligand excluded by PLIP PCW.27: 5 residues within 4Å: Ligands: PCW.34, PCW.36, PCW.42, PCW.46, 17F.52 Ligand excluded by PLIP PCW.28: 8 residues within 4Å: Ligands: 17F.22, PCW.26, PCW.30, PCW.31, PCW.48, 17F.54, 17F.83, 17F.84 Ligand excluded by PLIP PCW.29: 7 residues within 4Å: Ligands: PCW.19, PCW.26, PCW.47, PCW.48, 17F.50, PCW.60, PCW.74 Ligand excluded by PLIP PCW.30: 6 residues within 4Å: Ligands: PCW.24, PCW.28, PCW.31, PCW.48, 17F.50, 17F.51 Ligand excluded by PLIP PCW.31: 8 residues within 4Å: Ligands: PCW.28, PCW.30, PCW.38, PCW.43, 17F.50, 17F.54, PCW.73, 17F.79 Ligand excluded by PLIP PCW.32: 1 residues within 4Å: Ligands: 17F.53 Ligand excluded by PLIP PCW.33: 7 residues within 4Å: Ligands: PCW.4, PCW.17, PCW.20, PCW.25, PCW.39, PCW.62, PCW.81 Ligand excluded by PLIP PCW.34: 7 residues within 4Å: Ligands: PCW.1, PCW.27, PCW.36, PCW.42, PCW.45, PCW.46, PCW.47 Ligand excluded by PLIP PCW.35: 3 residues within 4Å: Ligands: PCW.18, PCW.41, PCW.49 Ligand excluded by PLIP PCW.36: 4 residues within 4Å: Ligands: PCW.27, PCW.34, PCW.42, 17F.63 Ligand excluded by PLIP PCW.37: 4 residues within 4Å: Ligands: PCW.1, PCW.19, PCW.42, PCW.47 Ligand excluded by PLIP PCW.38: 6 residues within 4Å: Ligands: PCW.31, 17F.54, PCW.71, PCW.72, PCW.73, 17F.79 Ligand excluded by PLIP PCW.39: 9 residues within 4Å: Ligands: PCW.6, PCW.20, PCW.33, PCW.40, PCW.41, PCW.49, PCW.69, PCW.75, PCW.81 Ligand excluded by PLIP PCW.40: 7 residues within 4Å: Ligands: PCW.3, PCW.4, PCW.17, PCW.18, PCW.20, PCW.21, PCW.39 Ligand excluded by PLIP PCW.41: 10 residues within 4Å: Ligands: PCW.6, PCW.8, PCW.20, PCW.35, PCW.39, PCW.49, 17F.53, PCW.69, PCW.75, PCW.82 Ligand excluded by PLIP PCW.42: 5 residues within 4Å: Ligands: PCW.27, PCW.34, PCW.36, PCW.37, PCW.57 Ligand excluded by PLIP PCW.43: 4 residues within 4Å: Ligands: PCW.31, PCW.44, 17F.54, PCW.73 Ligand excluded by PLIP PCW.44: 5 residues within 4Å: Ligands: 17F.22, PCW.43, 17F.53, 17F.54, PCW.82 Ligand excluded by PLIP PCW.45: 8 residues within 4Å: Ligands: PCW.26, PCW.34, PCW.46, PCW.47, PCW.57, PCW.62, PCW.76, 17F.80 Ligand excluded by PLIP PCW.46: 8 residues within 4Å: Ligands: PCW.25, PCW.27, PCW.34, PCW.45, PCW.57, PCW.62, 17F.63, PCW.82 Ligand excluded by PLIP PCW.47: 6 residues within 4Å: Ligands: PCW.19, PCW.29, PCW.34, PCW.37, PCW.45, PCW.48 Ligand excluded by PLIP PCW.48: 6 residues within 4Å: Ligands: PCW.19, PCW.26, PCW.28, PCW.29, PCW.30, PCW.47 Ligand excluded by PLIP PCW.49: 7 residues within 4Å: Ligands: PCW.35, PCW.39, PCW.41, 17F.53, PCW.75, PCW.81, PCW.82 Ligand excluded by PLIP PCW.57: 11 residues within 4Å: Chain D: K.178, S.181, K.182, T.183 Ligands: 17F.16, PCW.42, PCW.45, PCW.46, 17F.63, 17F.64, PCW.76 Ligand excluded by PLIP PCW.58: 5 residues within 4Å: Ligands: PCW.1, 17F.16, PCW.61, 17F.64, PCW.70 Ligand excluded by PLIP PCW.59: 7 residues within 4Å: Ligands: PCW.4, PCW.6, PCW.11, PCW.62, 17F.65, PCW.68, PCW.69 Ligand excluded by PLIP PCW.60: 8 residues within 4Å: Chain C: S.181, K.184 Ligands: PCW.9, PCW.29, 17F.64, PCW.70, PCW.74, 17F.79 Ligand excluded by PLIP PCW.61: 4 residues within 4Å: Chain C: K.176 Ligands: PCW.1, PCW.58, 17F.64 Ligand excluded by PLIP PCW.62: 10 residues within 4Å: Chain D: K.184 Ligands: PCW.33, PCW.45, PCW.46, PCW.59, PCW.68, PCW.69, PCW.76, PCW.81, PCW.82 Ligand excluded by PLIP PCW.68: 8 residues within 4Å: Ligands: PCW.59, PCW.62, PCW.69, PCW.72, PCW.75, PCW.77, 17F.78, PCW.81 Ligand excluded by PLIP PCW.69: 12 residues within 4Å: Ligands: PCW.6, PCW.39, PCW.41, PCW.59, PCW.62, 17F.65, PCW.68, PCW.75, 17F.78, PCW.81, PCW.82, 17F.84 Ligand excluded by PLIP PCW.70: 9 residues within 4Å: Chain D: K.176 Ligands: PCW.58, PCW.60, 17F.64, PCW.71, PCW.74, PCW.77, 17F.79, 17F.80 Ligand excluded by PLIP PCW.71: 9 residues within 4Å: Ligands: PCW.2, PCW.7, PCW.38, PCW.70, PCW.72, PCW.73, PCW.77, 17F.78, 17F.79 Ligand excluded by PLIP PCW.72: 6 residues within 4Å: Ligands: PCW.10, PCW.38, PCW.68, PCW.71, PCW.73, 17F.78 Ligand excluded by PLIP PCW.73: 9 residues within 4Å: Ligands: PCW.2, PCW.10, PCW.31, PCW.38, PCW.43, 17F.54, PCW.71, PCW.72, 17F.78 Ligand excluded by PLIP PCW.74: 5 residues within 4Å: Ligands: PCW.29, PCW.60, PCW.70, PCW.77, 17F.79 Ligand excluded by PLIP PCW.75: 9 residues within 4Å: Ligands: PCW.8, PCW.12, PCW.13, PCW.39, PCW.41, PCW.49, 17F.53, PCW.68, PCW.69 Ligand excluded by PLIP PCW.76: 9 residues within 4Å: Chain D: S.181, K.182, T.183 Ligands: PCW.45, PCW.57, PCW.62, 17F.63, 17F.80, PCW.82 Ligand excluded by PLIP PCW.77: 9 residues within 4Å: Chain D: K.176, K.177 Ligands: PCW.19, PCW.68, PCW.70, PCW.71, PCW.74, 17F.78, 17F.80 Ligand excluded by PLIP PCW.81: 9 residues within 4Å: Ligands: PCW.25, PCW.33, PCW.39, PCW.49, PCW.62, PCW.68, PCW.69, PCW.82, 17F.84 Ligand excluded by PLIP PCW.82: 11 residues within 4Å: Ligands: PCW.41, PCW.44, PCW.46, PCW.49, 17F.53, PCW.62, PCW.69, PCW.76, PCW.81, 17F.83, 17F.84 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.15: 6 residues within 4Å: Chain A: F.188 Chain D: T.183 Ligands: PCW.3, PCW.4, PCW.14, 17F.63 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:T.183, A:F.188 17F.16: 3 residues within 4Å: Chain A: L.170 Ligands: PCW.57, PCW.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.170 17F.22: 6 residues within 4Å: Ligands: PCW.10, PCW.28, PCW.44, 17F.54, 17F.83, 17F.84 No protein-ligand interaction detected (PLIP) 17F.50: 6 residues within 4Å: Ligands: PCW.23, PCW.24, PCW.29, PCW.30, PCW.31, 17F.51 No protein-ligand interaction detected (PLIP) 17F.51: 5 residues within 4Å: Chain B: W.67, M.71 Ligands: PCW.24, PCW.30, 17F.50 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.67 17F.52: 5 residues within 4Å: Chain B: Y.195, T.196, N.200 Ligands: PCW.21, PCW.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.195 17F.53: 8 residues within 4Å: Ligands: PCW.8, PCW.13, PCW.32, PCW.41, PCW.44, PCW.49, PCW.75, PCW.82 No protein-ligand interaction detected (PLIP) 17F.54: 8 residues within 4Å: Ligands: PCW.2, 17F.22, PCW.28, PCW.31, PCW.38, PCW.43, PCW.44, PCW.73 No protein-ligand interaction detected (PLIP) 17F.63: 9 residues within 4Å: Chain D: K.182, T.183, K.184 Ligands: PCW.14, 17F.15, PCW.36, PCW.46, PCW.57, PCW.76 No protein-ligand interaction detected (PLIP) 17F.64: 11 residues within 4Å: Chain C: K.178, K.179, K.180, S.181, K.182 Ligands: PCW.9, PCW.57, PCW.58, PCW.60, PCW.61, PCW.70 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.180, C:S.181, C:S.181 Salt bridges: C:K.179, C:K.179 17F.65: 6 residues within 4Å: Ligands: PCW.3, PCW.5, PCW.6, PCW.11, PCW.59, PCW.69 No protein-ligand interaction detected (PLIP) 17F.78: 7 residues within 4Å: Ligands: PCW.26, PCW.68, PCW.69, PCW.71, PCW.72, PCW.73, PCW.77 No protein-ligand interaction detected (PLIP) 17F.79: 7 residues within 4Å: Ligands: PCW.24, PCW.31, PCW.38, PCW.60, PCW.70, PCW.71, PCW.74 No protein-ligand interaction detected (PLIP) 17F.80: 9 residues within 4Å: Chain C: K.178 Chain D: K.176, K.178 Ligands: PCW.19, PCW.26, PCW.45, PCW.70, PCW.76, PCW.77 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:K.178, D:K.176, D:K.178 17F.83: 5 residues within 4Å: Ligands: 17F.22, PCW.26, PCW.28, PCW.82, 17F.84 No protein-ligand interaction detected (PLIP) 17F.84: 8 residues within 4Å: Ligands: 17F.22, PCW.25, PCW.26, PCW.28, PCW.69, PCW.81, PCW.82, 17F.83 No protein-ligand interaction detected (PLIP)

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

GSP.55: 23 residues within 4Å: Chain C: A.11, D.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, D.33, P.34, T.35, D.57, N.116, K.117, D.119, L.120, A.146, K.147 Ligands: MG.56 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:S.17, C:A.18, C:T.35, C:N.116, C:K.117, C:K.117, C:D.119, C:D.119, C:A.146, C:K.147, C:K.147 pi-Stacking: C:F.28, C:F.28 pi-Cation interactions: C:K.117 GSP.66: 25 residues within 4Å: Chain D: A.11, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, D.33, P.34, T.35, D.57, T.58, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.67 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:K.16, D:S.17, D:A.18, D:D.30, D:D.33, D:D.33, D:T.35, D:G.60, D:N.116, D:K.117, D:K.117, D:S.145, D:A.146, D:K.147 Salt bridges: D:K.16, D:D.119 pi-Stacking: D:F.28, D:F.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.56: 4 residues within 4Å: Chain C: S.17, T.35, D.57 Ligands: GSP.55 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.17, C:T.35, C:D.57 MG.67: 4 residues within 4Å: Chain D: S.17, T.35, D.57 Ligands: GSP.66 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.17, D:T.35, D:D.57

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

2020-04-15

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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