SMTL ID : 9bg1.1 (1 other biounit)

Tri-complex of Compound-3, KRAS G12V, and CypA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 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.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: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:Y.33, 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: 3 residues within 4Å: Chain A: S.18, T.36 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.2

1 x 01: (2R)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name)

01.3: 25 residues within 4Å: Chain A: Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, Y.72 Chain B: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, A.102, N.103, A.104, Q.112, F.114, L.123, H.127, R.149 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.58, B:F.61, B:F.61, B:A.102, B:F.114, B:L.123, A:I.37, A:A.60, A:Y.65, A:Y.65, A:Y.65, A:Y.65, A:M.68 Hydrogen bonds: B:R.56, B:Q.64, B:Q.64, B:N.103, B:N.103 Water bridges: B:R.56, B:R.149 Salt bridges: B:R.56 pi-Cation interactions: B:R.56 pi-Stacking: A:Y.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J. et al., Tri-complex of Compound-3, KRAS G12V, and CypA. To be published

Release Date

2024-06-12

Peptides

GTPase KRas: A
Peptidyl-prolyl cis-trans isomerase A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

GTPase KRas

Peptidyl-prolyl cis-trans isomerase A

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