SMTL ID : 6xha.1

Crystal Structure of KRAS-G12V (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 23 residues within 4Å: Chain A: A.12, V.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:G.16, A:K.17, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:Y.33, A:Y.33, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.42, Q.44, L.53 Chain B: N.13, T.87, T.131 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.131, A:Q.44 Water bridges: B:N.13, A:R.42 GOL.5: 4 residues within 4Å: Chain B: H.82, V.83, P.84, D.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.135 Water bridges: B:V.83 GOL.6: 2 residues within 4Å: Chain B: L.50, Q.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.76 GOL.7: 2 residues within 4Å: Chain B: H.28, N.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.18, T.36, D.58 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: D.55 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: L.11, K.14 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain B: H.88, C.114, C.117, C.133 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.88, B:C.114, B:C.117, B:C.133 ZN.9: 4 residues within 4Å: Chain B: C.101, C.104, H.122, C.125 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.101, B:C.104, B:H.122, B:C.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, T.H. et al., KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Nat Commun (2021)

Release Date

2021-01-13

Peptides

Isoform 2B of GTPase KRas: A
RAF proto-oncogene serine/threonine-protein kinase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 2B of GTPase KRas

RAF proto-oncogene serine/threonine-protein kinase

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