SMTL ID : 6zio.1

CRYSTAL STRUCTURE OF NRAS (C118S) IN COMPLEX WITH GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.3 MG.3: 2 residues within 4Å: Chain B: S.18 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.6, H2O.6, H2O.6, H2O.6 MG.4: 6 residues within 4Å: Chain B: A.19, I.22, Q.23, H.28, F.29, V.30 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.19, B:H.28

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 20 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, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:S.18, A:D.31, A:Y.33, A:Y.33, A:D.58 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 GDP.5: 20 residues within 4Å: Chain B: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:A.12, B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:V.30, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:S.18, B:D.31, B:Y.33, B:K.148 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29, B:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D. et al., Drugging all RAS isoforms with one pocket. Future Med Chem (2020)

Release Date

2020-08-19

Peptides

GTPase NRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase NRas

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