SMTL ID : 6pts.1

NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)

Coordinates

PDB Format Compare

Method

SOLUTION NMR

Oligo State

hetero-2-1-1-mer

Ligands

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

PCW.1: 5 residues within 4Å: Ligands: PCW.27, PCW.30, PCW.35, PCW.68, PCW.74 Ligand excluded by PLIP PCW.2: 9 residues within 4Å: Chain A: F.14 Chain C: Q.131, F.141, I.142 Ligands: PCW.13, PCW.28, PCW.59, PCW.73, 17F.79 Ligand excluded by PLIP PCW.3: 5 residues within 4Å: Ligands: PCW.6, PCW.50, PCW.54, PCW.56, PCW.58 Ligand excluded by PLIP PCW.4: 6 residues within 4Å: Chain A: L.39, M.43 Ligands: PCW.7, 17F.48, PCW.59, PCW.60 Ligand excluded by PLIP PCW.5: 3 residues within 4Å: Ligands: PCW.14, PCW.52, 17F.78 Ligand excluded by PLIP PCW.6: 5 residues within 4Å: Chain A: D.46, V.50 Ligands: PCW.3, PCW.58, PCW.60 Ligand excluded by PLIP PCW.7: 4 residues within 4Å: Ligands: PCW.4, 17F.48, PCW.59, PCW.60 Ligand excluded by PLIP PCW.8: 2 residues within 4Å: Ligands: 17F.9, 17F.77 Ligand excluded by PLIP PCW.11: 7 residues within 4Å: Ligands: PCW.15, PCW.16, PCW.33, 17F.47, PCW.51, PCW.70, PCW.81 Ligand excluded by PLIP PCW.12: 5 residues within 4Å: Ligands: PCW.14, PCW.21, PCW.40, PCW.41, PCW.52 Ligand excluded by PLIP PCW.13: 6 residues within 4Å: Chain A: V.10, F.14 Ligands: PCW.2, PCW.15, PCW.28, PCW.33 Ligand excluded by PLIP PCW.14: 7 residues within 4Å: Ligands: PCW.5, PCW.12, PCW.21, PCW.30, PCW.40, PCW.41, PCW.61 Ligand excluded by PLIP PCW.15: 6 residues within 4Å: Ligands: PCW.11, PCW.13, PCW.32, PCW.33, PCW.34, PCW.81 Ligand excluded by PLIP PCW.16: 3 residues within 4Å: Ligands: PCW.11, PCW.33, 17F.47 Ligand excluded by PLIP PCW.17: 6 residues within 4Å: Ligands: PCW.20, PCW.22, PCW.27, PCW.38, PCW.39, 17F.77 Ligand excluded by PLIP PCW.18: 5 residues within 4Å: Chain A: L.120 Chain B: K.53, Y.57 Ligands: PCW.19, 17F.43 Ligand excluded by PLIP PCW.19: 7 residues within 4Å: Chain B: F.61, K.64 Ligands: PCW.18, PCW.24, 17F.43, 17F.46, 17F.63 Ligand excluded by PLIP PCW.20: 5 residues within 4Å: Ligands: PCW.17, PCW.21, 17F.45, PCW.81, PCW.82 Ligand excluded by PLIP PCW.21: 11 residues within 4Å: Ligands: PCW.12, PCW.14, PCW.20, PCW.23, PCW.39, PCW.41, 17F.44, 17F.45, 17F.62, PCW.75, 17F.80 Ligand excluded by PLIP PCW.22: 6 residues within 4Å: Ligands: PCW.17, PCW.27, PCW.29, PCW.35, 17F.47, 17F.77 Ligand excluded by PLIP PCW.23: 6 residues within 4Å: Ligands: PCW.21, PCW.25, PCW.41, 17F.44, 17F.45, 17F.64 Ligand excluded by PLIP PCW.24: 5 residues within 4Å: Ligands: PCW.19, PCW.25, PCW.41, 17F.43, 17F.46 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Ligands: PCW.23, PCW.24, PCW.31, PCW.36, 17F.43, 17F.49, PCW.55, PCW.56, 17F.63 Ligand excluded by PLIP PCW.26: 1 residues within 4Å: Ligands: 17F.48 Ligand excluded by PLIP PCW.27: 8 residues within 4Å: Ligands: PCW.1, 17F.10, PCW.17, PCW.22, PCW.29, PCW.35, PCW.39, PCW.40 Ligand excluded by PLIP PCW.28: 4 residues within 4Å: Ligands: PCW.2, PCW.13, PCW.34, PCW.42 Ligand excluded by PLIP PCW.29: 4 residues within 4Å: Ligands: PCW.22, PCW.27, PCW.35, 17F.77 Ligand excluded by PLIP PCW.30: 5 residues within 4Å: Ligands: PCW.1, PCW.14, PCW.35, PCW.39, PCW.40 Ligand excluded by PLIP PCW.31: 5 residues within 4Å: Ligands: PCW.25, 17F.49, PCW.54, PCW.55, PCW.56 Ligand excluded by PLIP PCW.32: 8 residues within 4Å: Ligands: PCW.15, PCW.33, PCW.34, PCW.42, PCW.60, PCW.69, PCW.81, PCW.82 Ligand excluded by PLIP PCW.33: 6 residues within 4Å: Ligands: PCW.11, PCW.13, PCW.15, PCW.16, PCW.32, PCW.51 Ligand excluded by PLIP PCW.34: 8 residues within 4Å: Ligands: PCW.15, PCW.28, PCW.32, PCW.38, PCW.42, PCW.69, PCW.73, 17F.79 Ligand excluded by PLIP PCW.35: 6 residues within 4Å: Ligands: PCW.1, 17F.10, PCW.22, PCW.27, PCW.29, PCW.30 Ligand excluded by PLIP PCW.36: 3 residues within 4Å: Ligands: PCW.25, PCW.37, 17F.49 Ligand excluded by PLIP PCW.37: 5 residues within 4Å: Ligands: PCW.36, PCW.38, 17F.48, 17F.49, 17F.64 Ligand excluded by PLIP PCW.38: 9 residues within 4Å: Ligands: PCW.17, PCW.34, PCW.37, PCW.42, 17F.44, 17F.45, 17F.62, PCW.72, PCW.82 Ligand excluded by PLIP PCW.39: 8 residues within 4Å: Ligands: PCW.17, PCW.21, PCW.27, PCW.30, PCW.40, PCW.67, PCW.75, 17F.77 Ligand excluded by PLIP PCW.40: 6 residues within 4Å: Ligands: PCW.12, PCW.14, PCW.27, PCW.30, PCW.39, PCW.41 Ligand excluded by PLIP PCW.41: 6 residues within 4Å: Ligands: PCW.12, PCW.14, PCW.21, PCW.23, PCW.24, PCW.40 Ligand excluded by PLIP PCW.42: 8 residues within 4Å: Ligands: PCW.28, PCW.32, PCW.34, PCW.38, 17F.48, PCW.60, PCW.72, PCW.82 Ligand excluded by PLIP PCW.50: 4 residues within 4Å: Ligands: PCW.3, PCW.54, PCW.56, PCW.58 Ligand excluded by PLIP PCW.51: 7 residues within 4Å: Chain C: R.135, K.165 Ligands: 17F.9, PCW.11, PCW.33, PCW.70, PCW.73 Ligand excluded by PLIP PCW.52: 4 residues within 4Å: Ligands: PCW.5, PCW.12, PCW.53, PCW.57 Ligand excluded by PLIP PCW.53: 8 residues within 4Å: Chain D: Q.101 Ligands: PCW.52, PCW.57, PCW.61, 17F.63, PCW.68, 17F.78, 17F.80 Ligand excluded by PLIP PCW.54: 9 residues within 4Å: Ligands: PCW.3, PCW.31, 17F.49, PCW.50, PCW.55, PCW.56, PCW.61, 17F.62, 17F.63 Ligand excluded by PLIP PCW.55: 10 residues within 4Å: Chain D: N.106, E.119, H.120 Ligands: PCW.25, PCW.31, 17F.45, PCW.54, PCW.56, PCW.58, 17F.62 Ligand excluded by PLIP PCW.56: 8 residues within 4Å: Ligands: PCW.3, PCW.25, PCW.31, 17F.49, PCW.50, PCW.54, PCW.55, PCW.58 Ligand excluded by PLIP PCW.57: 5 residues within 4Å: Ligands: PCW.52, PCW.53, PCW.61, 17F.63, 17F.78 Ligand excluded by PLIP PCW.58: 7 residues within 4Å: Ligands: PCW.3, PCW.6, PCW.50, PCW.55, PCW.56, 17F.62, 17F.64 Ligand excluded by PLIP PCW.59: 14 residues within 4Å: Chain C: Q.150, G.151, V.152, D.153, D.154 Chain D: L.92 Ligands: PCW.2, PCW.4, PCW.7, PCW.60, PCW.69, PCW.72, PCW.73, 17F.79 Ligand excluded by PLIP PCW.60: 11 residues within 4Å: Chain D: T.90 Ligands: PCW.4, PCW.6, PCW.7, PCW.32, PCW.42, 17F.48, PCW.59, PCW.69, PCW.71, PCW.72 Ligand excluded by PLIP PCW.61: 9 residues within 4Å: Chain D: K.102 Ligands: PCW.14, PCW.53, PCW.54, PCW.57, 17F.62, 17F.63, 17F.78, 17F.80 Ligand excluded by PLIP PCW.67: 8 residues within 4Å: Chain D: C.100, Q.101 Ligands: 17F.10, PCW.39, PCW.75, 17F.77, 17F.78, 17F.80 Ligand excluded by PLIP PCW.68: 5 residues within 4Å: Ligands: PCW.1, 17F.10, PCW.53, PCW.74, 17F.78 Ligand excluded by PLIP PCW.69: 13 residues within 4Å: Chain C: D.47, D.154, Y.157, R.161 Chain D: K.93 Ligands: PCW.32, PCW.34, PCW.59, PCW.60, PCW.70, PCW.72, PCW.73, PCW.76 Ligand excluded by PLIP PCW.70: 8 residues within 4Å: Chain C: K.165, E.168, K.172 Ligands: 17F.9, PCW.11, PCW.51, PCW.69, PCW.76 Ligand excluded by PLIP PCW.71: 8 residues within 4Å: Chain D: F.103 Ligands: PCW.60, 17F.62, PCW.72, PCW.75, PCW.76, 17F.79, PCW.82 Ligand excluded by PLIP PCW.72: 12 residues within 4Å: Chain D: T.90, F.91, L.92 Ligands: PCW.38, PCW.42, 17F.45, PCW.59, PCW.60, PCW.69, PCW.71, 17F.79, PCW.82 Ligand excluded by PLIP PCW.73: 10 residues within 4Å: Chain C: T.158, R.161, E.162, K.165 Ligands: PCW.2, PCW.34, PCW.51, PCW.59, PCW.69, 17F.79 Ligand excluded by PLIP PCW.74: 4 residues within 4Å: Ligands: PCW.1, PCW.68, 17F.78, 17F.80 Ligand excluded by PLIP PCW.75: 9 residues within 4Å: Chain D: F.96, K.102, F.103 Ligands: PCW.21, PCW.39, PCW.67, PCW.71, PCW.76, 17F.80 Ligand excluded by PLIP PCW.76: 8 residues within 4Å: Chain D: F.96 Ligands: PCW.69, PCW.70, PCW.71, PCW.75, 17F.79, PCW.81, PCW.82 Ligand excluded by PLIP PCW.81: 6 residues within 4Å: Ligands: PCW.11, PCW.15, PCW.20, PCW.32, PCW.76, PCW.82 Ligand excluded by PLIP PCW.82: 9 residues within 4Å: Ligands: PCW.20, PCW.32, PCW.38, PCW.42, PCW.71, PCW.72, PCW.76, 17F.79, PCW.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-covalent)(Non-functional Binders)

17F.9: 6 residues within 4Å: Chain C: K.169, K.172 Ligands: PCW.8, PCW.51, PCW.70, 17F.77 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.169, C:K.172 17F.10: 4 residues within 4Å: Ligands: PCW.27, PCW.35, PCW.67, PCW.68 No protein-ligand interaction detected (PLIP) 17F.43: 7 residues within 4Å: Chain B: W.65 Ligands: PCW.18, PCW.19, PCW.24, PCW.25, 17F.46, 17F.63 No protein-ligand interaction detected (PLIP) 17F.44: 6 residues within 4Å: Ligands: PCW.21, PCW.23, PCW.38, 17F.45, 17F.62, 17F.64 No protein-ligand interaction detected (PLIP) 17F.45: 9 residues within 4Å: Ligands: PCW.20, PCW.21, PCW.23, PCW.38, 17F.44, PCW.55, 17F.62, 17F.64, PCW.72 No protein-ligand interaction detected (PLIP) 17F.46: 4 residues within 4Å: Chain B: W.65 Ligands: PCW.19, PCW.24, 17F.43 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.65 17F.47: 6 residues within 4Å: Chain B: L.190, Y.193, N.198 Ligands: PCW.11, PCW.16, PCW.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.190, B:Y.193 17F.48: 6 residues within 4Å: Ligands: PCW.4, PCW.7, PCW.26, PCW.37, PCW.42, PCW.60 No protein-ligand interaction detected (PLIP) 17F.49: 7 residues within 4Å: Ligands: PCW.25, PCW.31, PCW.36, PCW.37, PCW.54, PCW.56, 17F.64 No protein-ligand interaction detected (PLIP) 17F.62: 9 residues within 4Å: Ligands: PCW.21, PCW.38, 17F.44, 17F.45, PCW.54, PCW.55, PCW.58, PCW.61, PCW.71 No protein-ligand interaction detected (PLIP) 17F.63: 7 residues within 4Å: Ligands: PCW.19, PCW.25, 17F.43, PCW.53, PCW.54, PCW.57, PCW.61 No protein-ligand interaction detected (PLIP) 17F.64: 6 residues within 4Å: Ligands: PCW.23, PCW.37, 17F.44, 17F.45, 17F.49, PCW.58 No protein-ligand interaction detected (PLIP) 17F.77: 7 residues within 4Å: Ligands: PCW.8, 17F.9, PCW.17, PCW.22, PCW.29, PCW.39, PCW.67 No protein-ligand interaction detected (PLIP) 17F.78: 8 residues within 4Å: Ligands: PCW.5, PCW.53, PCW.57, PCW.61, PCW.67, PCW.68, PCW.74, 17F.80 No protein-ligand interaction detected (PLIP) 17F.79: 11 residues within 4Å: Chain C: I.142, G.151, D.154 Ligands: PCW.2, PCW.34, PCW.59, PCW.71, PCW.72, PCW.73, PCW.76, PCW.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.154 17F.80: 9 residues within 4Å: Chain D: Q.101, K.102 Ligands: PCW.21, PCW.53, PCW.61, PCW.67, PCW.74, PCW.75, 17F.78 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.102

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

GNP.65: 22 residues within 4Å: Chain C: G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, Y.32, D.33, P.34, T.35, T.58, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.66 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.13, C:G.15, C:K.16, C:K.16, C:S.17, C:A.18, C:Y.32, C:T.35, C:T.35, C:T.58, C:N.116, C:A.146, C:K.147 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.66: 6 residues within 4Å: Chain C: K.16, S.17, D.33, T.35, D.57 Ligands: GNP.65 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.17, C:T.35

2 x ZN: ZINC ION(Non-covalent)

ZN.83: 4 residues within 4Å: Chain D: C.97, C.100, H.118, C.121 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:C.100, D:H.118, D:C.121 ZN.84: 5 residues within 4Å: Chain D: H.84, C.110, C.113, Y.115, C.129 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.84, D:C.110, D:C.113, D:C.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, Z. et al., Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-05-13

Peptides

Apolipoprotein A-I: AB
GTPase KRas: C
RAF proto-oncogene serine/threonine-protein kinase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Apolipoprotein A-I

GTPase KRas

RAF proto-oncogene serine/threonine-protein kinase

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