SMTL ID : 6xhb.1

Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:D.34, A:T.36, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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

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

CL.3: 2 residues within 4Å: Chain B: T.87, T.131 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: Q.23 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: K.58 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: H.82, V.83, P.84, D.135 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.135, B:D.135 Water bridges: B:H.82, B:H.82, B:V.83 GOL.10: 4 residues within 4Å: Chain B: K.93, F.95, L.96, K.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.93, B:L.96, B:K.97

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 3 residues within 4Å: Chain B: L.11, N.13, K.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.11, B:K.14 Water bridges: B:Q.76

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.8: 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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

RAF proto-oncogene serine/threonine-protein kinase

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