SMTL ID : 5ufe.1

Wild-type K-Ras(GNP)/R11.1.6 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 22 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, D.33, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: CD.6, CL.8, MG.11 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:S.17, A:A.18, A:D.30, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:E.31, A:D.57, A:G.60, A:G.60 Salt bridges: A:D.119

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 2 residues within 4Å: Chain A: E.31 Ligands: CL.8 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.31, H2O.1, H2O.1, H2O.3 CA.3: 1 residues within 4Å: Chain A: D.108 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.108, A:D.108, H2O.1, H2O.2, H2O.2 CA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x CD: CADMIUM ION(Non-covalent)

CD.4: 5 residues within 4Å: Chain A: I.36, E.37, E.62, M.67 Chain B: K.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.37, A:E.37, A:E.62, A:E.62, H2O.3 CD.5: 2 residues within 4Å: Chain A: C.118 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.118, A:C.118 CD.6: 2 residues within 4Å: Chain A: D.33 Ligands: GNP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.33, A:D.33, H2O.3 CD.7: 1 residues within 4Å: Chain A: E.91 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.91, A:E.91, H2O.3, H2O.3

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

CL.8: 2 residues within 4Å: Ligands: GNP.1, CA.2 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: D.119, S.145, T.148 Ligands: CD.5 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: H.95 Ligands: CO.14 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 2 residues within 4Å: Chain A: S.17 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1

3 x CO: COBALT (II) ION(Non-covalent)

CO.12: 3 residues within 4Å: Chain A: E.3, K.5, E.76 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.3, A:E.76, A:E.76, H2O.2, H2O.2 CO.13: 1 residues within 4Å: Chain A: H.27 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.27, H2O.1 CO.14: 3 residues within 4Å: Chain A: H.95, E.98 Ligands: CL.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, A:E.98, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kauke, M.J. et al., An engineered protein antagonist of K-Ras/B-Raf interaction. Sci Rep (2017)

Release Date

2017-08-02

Peptides

GTPase KRas: A
R11.1.6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

R11.1.6

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