SMTL ID : 6ptw.1

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

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-covalent)(Non-functional Binders)

PCW.1: 5 residues within 4Å: Chain A: A.153 Ligands: PCW.26, PCW.29, PCW.55, PCW.63 Ligand excluded by PLIP PCW.2: 5 residues within 4Å: Ligands: PCW.5, 17F.46, PCW.60, PCW.64, PCW.66 Ligand excluded by PLIP PCW.3: 4 residues within 4Å: Ligands: PCW.7, PCW.59, PCW.65, 17F.74 Ligand excluded by PLIP PCW.4: 12 residues within 4Å: Chain A: F.14, L.17, R.18, W.29, L.32 Chain B: H.156 Chain D: R.4, E.70 Ligands: PCW.11, PCW.48, PCW.62, 17F.76 Ligand excluded by PLIP PCW.5: 6 residues within 4Å: Chain C: K.172, T.183 Ligands: PCW.2, PCW.8, PCW.60, PCW.66 Ligand excluded by PLIP PCW.6: 7 residues within 4Å: Chain A: L.39 Chain C: K.104 Ligands: PCW.33, 17F.44, PCW.48, PCW.49, PCW.50 Ligand excluded by PLIP PCW.7: 3 residues within 4Å: Ligands: PCW.3, PCW.12, 17F.74 Ligand excluded by PLIP PCW.8: 11 residues within 4Å: Chain A: D.46, V.50 Chain B: Y.123 Chain C: K.172, K.176 Ligands: PCW.5, PCW.47, PCW.49, PCW.58, PCW.66, PCW.80 Ligand excluded by PLIP PCW.10: 6 residues within 4Å: Ligands: PCW.13, PCW.32, 17F.43, PCW.57, PCW.70, PCW.78 Ligand excluded by PLIP PCW.11: 6 residues within 4Å: Chain A: F.14 Chain B: H.156 Ligands: PCW.4, PCW.13, PCW.27, PCW.32 Ligand excluded by PLIP PCW.12: 6 residues within 4Å: Ligands: PCW.7, PCW.19, PCW.22, PCW.29, PCW.38, PCW.39 Ligand excluded by PLIP PCW.13: 6 residues within 4Å: Chain A: L.3 Ligands: PCW.10, PCW.11, PCW.31, PCW.32, PCW.78 Ligand excluded by PLIP PCW.14: 2 residues within 4Å: Ligands: PCW.32, 17F.43 Ligand excluded by PLIP PCW.15: 5 residues within 4Å: Ligands: PCW.18, PCW.20, PCW.37, 17F.73, PCW.80 Ligand excluded by PLIP PCW.16: 3 residues within 4Å: Ligands: PCW.17, 17F.41, 17F.75 Ligand excluded by PLIP PCW.17: 7 residues within 4Å: Chain A: L.116 Ligands: PCW.16, PCW.23, 17F.41, 17F.42, PCW.65, 17F.75 Ligand excluded by PLIP PCW.18: 6 residues within 4Å: Ligands: PCW.15, PCW.19, PCW.78, PCW.79, PCW.80, 17F.82 Ligand excluded by PLIP PCW.19: 11 residues within 4Å: Ligands: PCW.12, PCW.18, PCW.21, PCW.37, PCW.39, PCW.67, PCW.69, 17F.72, 17F.77, 17F.81, 17F.82 Ligand excluded by PLIP PCW.20: 7 residues within 4Å: Ligands: PCW.15, PCW.26, PCW.28, PCW.34, PCW.37, 17F.43, 17F.73 Ligand excluded by PLIP PCW.21: 8 residues within 4Å: Ligands: PCW.19, PCW.23, PCW.24, PCW.39, 17F.45, 17F.46, 17F.81, 17F.82 Ligand excluded by PLIP PCW.22: 3 residues within 4Å: Ligands: PCW.12, PCW.38, PCW.39 Ligand excluded by PLIP PCW.23: 6 residues within 4Å: Ligands: PCW.17, PCW.21, PCW.24, PCW.39, 17F.41, 17F.42 Ligand excluded by PLIP PCW.24: 8 residues within 4Å: Ligands: PCW.21, PCW.23, PCW.30, PCW.35, 17F.41, 17F.46, PCW.64, 17F.75 Ligand excluded by PLIP PCW.25: 2 residues within 4Å: Ligands: 17F.44, PCW.49 Ligand excluded by PLIP PCW.26: 8 residues within 4Å: Ligands: PCW.1, PCW.20, PCW.28, PCW.34, PCW.37, PCW.38, PCW.53, PCW.55 Ligand excluded by PLIP PCW.27: 3 residues within 4Å: Ligands: PCW.11, PCW.33, PCW.40 Ligand excluded by PLIP PCW.28: 4 residues within 4Å: Ligands: PCW.20, PCW.26, PCW.34, 17F.73 Ligand excluded by PLIP PCW.29: 4 residues within 4Å: Ligands: PCW.1, PCW.12, PCW.34, PCW.38 Ligand excluded by PLIP PCW.30: 4 residues within 4Å: Ligands: PCW.24, 17F.46, PCW.61, PCW.64 Ligand excluded by PLIP PCW.31: 9 residues within 4Å: Ligands: PCW.13, PCW.32, PCW.33, PCW.40, PCW.47, PCW.49, 17F.76, PCW.78, PCW.79 Ligand excluded by PLIP PCW.32: 8 residues within 4Å: Ligands: PCW.10, PCW.11, PCW.13, PCW.14, PCW.31, PCW.54, PCW.57, PCW.78 Ligand excluded by PLIP PCW.33: 9 residues within 4Å: Ligands: PCW.6, PCW.27, PCW.31, PCW.40, 17F.44, PCW.49, PCW.62, 17F.76, PCW.80 Ligand excluded by PLIP PCW.34: 7 residues within 4Å: Chain B: F.14 Ligands: 17F.9, PCW.20, PCW.26, PCW.28, PCW.29, PCW.53 Ligand excluded by PLIP PCW.35: 3 residues within 4Å: Ligands: PCW.24, PCW.36, 17F.46 Ligand excluded by PLIP PCW.36: 5 residues within 4Å: Ligands: PCW.35, 17F.44, 17F.45, 17F.46, PCW.80 Ligand excluded by PLIP PCW.37: 7 residues within 4Å: Ligands: PCW.15, PCW.19, PCW.20, PCW.26, PCW.38, PCW.53, 17F.77 Ligand excluded by PLIP PCW.38: 7 residues within 4Å: Ligands: PCW.12, PCW.22, PCW.26, PCW.29, PCW.37, PCW.39, 17F.77 Ligand excluded by PLIP PCW.39: 6 residues within 4Å: Ligands: PCW.12, PCW.19, PCW.21, PCW.22, PCW.23, PCW.38 Ligand excluded by PLIP PCW.40: 6 residues within 4Å: Ligands: PCW.27, PCW.31, PCW.33, 17F.44, PCW.79, PCW.80 Ligand excluded by PLIP PCW.47: 14 residues within 4Å: Chain C: E.3 Ligands: PCW.8, PCW.31, PCW.48, PCW.49, PCW.50, PCW.56, PCW.58, PCW.62, PCW.67, PCW.68, 17F.76, PCW.79, PCW.80 Ligand excluded by PLIP PCW.48: 11 residues within 4Å: Chain C: E.3, K.5, T.74 Ligands: PCW.4, PCW.6, PCW.47, PCW.49, PCW.56, PCW.58, PCW.62, 17F.76 Ligand excluded by PLIP PCW.49: 13 residues within 4Å: Chain C: K.167, S.171 Ligands: PCW.6, PCW.8, PCW.25, PCW.31, PCW.33, 17F.44, PCW.47, PCW.48, PCW.50, PCW.56, PCW.58 Ligand excluded by PLIP PCW.50: 3 residues within 4Å: Ligands: PCW.6, PCW.47, PCW.49 Ligand excluded by PLIP PCW.53: 11 residues within 4Å: Chain D: I.99, K.124 Ligands: 17F.9, PCW.26, PCW.34, PCW.37, PCW.55, PCW.58, PCW.67, 17F.73, 17F.77 Ligand excluded by PLIP PCW.54: 12 residues within 4Å: Chain D: L.47, K.51, G.52, K.53, K.54, L.81, W.132 Ligands: PCW.32, PCW.57, PCW.62, PCW.70, 17F.71 Ligand excluded by PLIP PCW.55: 6 residues within 4Å: Ligands: PCW.1, 17F.9, PCW.26, PCW.53, PCW.63, 17F.74 Ligand excluded by PLIP PCW.56: 17 residues within 4Å: Chain C: M.1, E.3, L.52 Chain D: K.10, T.127, M.128, V.130, D.131, W.132 Ligands: PCW.47, PCW.48, PCW.49, PCW.57, PCW.58, PCW.62, PCW.68, 17F.76 Ligand excluded by PLIP PCW.57: 7 residues within 4Å: Chain D: L.81 Ligands: PCW.10, PCW.32, PCW.54, PCW.56, PCW.70, 17F.71 Ligand excluded by PLIP PCW.58: 13 residues within 4Å: Chain D: F.96 Ligands: PCW.8, PCW.47, PCW.48, PCW.49, PCW.53, PCW.56, PCW.61, PCW.67, PCW.68, 17F.72, 17F.76, PCW.80 Ligand excluded by PLIP PCW.59: 6 residues within 4Å: Ligands: PCW.3, PCW.65, PCW.69, 17F.74, 17F.75, 17F.77 Ligand excluded by PLIP PCW.60: 8 residues within 4Å: Ligands: PCW.2, PCW.5, 17F.46, PCW.61, PCW.64, PCW.69, 17F.72, 17F.75 Ligand excluded by PLIP PCW.61: 6 residues within 4Å: Chain D: F.96 Ligands: PCW.30, PCW.58, PCW.60, PCW.66, 17F.72 Ligand excluded by PLIP PCW.62: 8 residues within 4Å: Chain D: W.132 Ligands: PCW.4, PCW.33, PCW.47, PCW.48, PCW.54, PCW.56, 17F.76 Ligand excluded by PLIP PCW.63: 3 residues within 4Å: Chain D: E.119 Ligands: PCW.1, PCW.55 Ligand excluded by PLIP PCW.64: 6 residues within 4Å: Ligands: PCW.2, PCW.24, PCW.30, 17F.46, PCW.60, PCW.66 Ligand excluded by PLIP PCW.65: 5 residues within 4Å: Ligands: PCW.3, PCW.17, PCW.59, PCW.69, 17F.75 Ligand excluded by PLIP PCW.66: 7 residues within 4Å: Chain C: C.185 Ligands: PCW.2, PCW.5, PCW.8, 17F.45, PCW.61, PCW.64 Ligand excluded by PLIP PCW.67: 12 residues within 4Å: Chain C: M.1 Chain D: D.98, I.99, Q.101, P.126 Ligands: PCW.19, PCW.47, PCW.53, PCW.58, PCW.68, 17F.72, PCW.80 Ligand excluded by PLIP PCW.68: 12 residues within 4Å: Chain C: M.1 Chain D: Y.115, P.126, T.127, W.132 Ligands: PCW.47, PCW.56, PCW.58, PCW.67, 17F.71, PCW.79, 17F.81 Ligand excluded by PLIP PCW.69: 10 residues within 4Å: Chain D: F.96, Q.101, K.102, F.103 Ligands: PCW.19, PCW.59, PCW.60, PCW.65, 17F.72, 17F.77 Ligand excluded by PLIP PCW.70: 6 residues within 4Å: Chain D: V.79, T.83 Ligands: PCW.10, PCW.54, PCW.57, 17F.71 Ligand excluded by PLIP PCW.78: 6 residues within 4Å: Ligands: PCW.10, PCW.13, PCW.18, PCW.31, PCW.32, PCW.79 Ligand excluded by PLIP PCW.79: 8 residues within 4Å: Ligands: PCW.18, PCW.31, PCW.40, PCW.47, PCW.68, PCW.78, PCW.80, 17F.82 Ligand excluded by PLIP PCW.80: 14 residues within 4Å: Ligands: PCW.8, PCW.15, PCW.18, PCW.33, PCW.36, PCW.40, 17F.44, PCW.47, PCW.58, PCW.67, 17F.72, PCW.79, 17F.81, 17F.82 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 A: L.168, L.171 Ligands: PCW.34, PCW.53, PCW.55, 17F.73 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.168, A:L.171, A:L.171 17F.41: 6 residues within 4Å: Ligands: PCW.16, PCW.17, PCW.23, PCW.24, 17F.42, 17F.75 No protein-ligand interaction detected (PLIP) 17F.42: 5 residues within 4Å: Chain B: F.61, W.65 Ligands: PCW.17, PCW.23, 17F.41 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.61 17F.43: 4 residues within 4Å: Chain B: Y.193 Ligands: PCW.10, PCW.14, PCW.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.193 17F.44: 7 residues within 4Å: Ligands: PCW.6, PCW.25, PCW.33, PCW.36, PCW.40, PCW.49, PCW.80 No protein-ligand interaction detected (PLIP) 17F.45: 6 residues within 4Å: Ligands: PCW.21, PCW.36, 17F.46, PCW.66, 17F.81, 17F.82 No protein-ligand interaction detected (PLIP) 17F.46: 9 residues within 4Å: Ligands: PCW.2, PCW.21, PCW.24, PCW.30, PCW.35, PCW.36, 17F.45, PCW.60, PCW.64 No protein-ligand interaction detected (PLIP) 17F.71: 5 residues within 4Å: Chain D: K.53 Ligands: PCW.54, PCW.57, PCW.68, PCW.70 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.53 17F.72: 9 residues within 4Å: Chain D: Q.101 Ligands: PCW.19, PCW.58, PCW.60, PCW.61, PCW.67, PCW.69, PCW.80, 17F.82 No protein-ligand interaction detected (PLIP) 17F.73: 5 residues within 4Å: Ligands: 17F.9, PCW.15, PCW.20, PCW.28, PCW.53 No protein-ligand interaction detected (PLIP) 17F.74: 6 residues within 4Å: Chain D: H.120 Ligands: PCW.3, PCW.7, PCW.55, PCW.59, 17F.77 No protein-ligand interaction detected (PLIP) 17F.75: 7 residues within 4Å: Ligands: PCW.16, PCW.17, PCW.24, 17F.41, PCW.59, PCW.60, PCW.65 No protein-ligand interaction detected (PLIP) 17F.76: 8 residues within 4Å: Ligands: PCW.4, PCW.31, PCW.33, PCW.47, PCW.48, PCW.56, PCW.58, PCW.62 No protein-ligand interaction detected (PLIP) 17F.77: 11 residues within 4Å: Chain D: K.102, L.105, H.120, K.124 Ligands: PCW.19, PCW.37, PCW.38, PCW.53, PCW.59, PCW.69, 17F.74 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:K.102, D:K.102, D:H.120 17F.81: 6 residues within 4Å: Ligands: PCW.19, PCW.21, 17F.45, PCW.68, PCW.80, 17F.82 No protein-ligand interaction detected (PLIP) 17F.82: 8 residues within 4Å: Ligands: PCW.18, PCW.19, PCW.21, 17F.45, 17F.72, PCW.79, PCW.80, 17F.81 No protein-ligand interaction detected (PLIP)

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

GNP.51: 24 residues within 4Å: Chain C: A.11, G.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, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.52 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:A.11, C:G.13, C:V.14, C:G.15, C:K.16, C:K.16, C:S.17, C:A.18, C:V.29, C:D.30, C:Y.32, C:T.35, C:G.60, C:N.116, C:K.117, C:S.145, C:A.146, C:K.147 pi-Cation interactions: C:K.117

1 x MG: MAGNESIUM ION(Non-covalent)

MG.52: 6 residues within 4Å: Chain C: K.16, S.17, D.33, T.35, D.57 Ligands: GNP.51 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: 6 residues within 4Å: Chain D: C.97, I.99, C.100, H.118, C.121, K.124 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:C.100, D:H.118, D:C.121 ZN.84: 7 residues within 4Å: Chain D: H.84, N.85, C.110, C.113, G.114, 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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