SMTL ID : 9i5e.1

A Coiled Coil Module Strategy for High-Resolution Cryo-EM Structures of Small Proteins for Drug Discovery

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.77 Å

Oligo State

hetero-2-2-mer

Ligands

2 x M1X: {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile(Covalent)

M1X.1: 11 residues within 4Å: Chain A: V.9, G.10, A.11, C.12, T.58, G.60, M.72, D.92, Y.96, Q.99, I.100 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.58, A:Q.99, A:I.100 Hydrogen bonds: A:G.10, A:Y.96 Salt bridges: A:D.92 pi-Stacking: A:Y.96 M1X.6: 13 residues within 4Å: Chain D: V.9, G.10, A.11, C.12, K.16, T.58, G.60, E.63, M.72, D.92, Y.96, Q.99, I.100 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.58, D:Q.99, D:I.100 Hydrogen bonds: D:G.10, D:K.16, D:Y.96 pi-Stacking: D:Y.96

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

GDP.2: 16 residues within 4Å: Chain A: A.11, C.12, G.13, G.15, K.16, S.17, F.28, D.30, E.31, P.34, K.117, L.120, P.121, A.146, K.147 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.13, A:K.16, A:K.117, A:A.146, A:K.147, A:K.147, A:K.147 GDP.4: 17 residues within 4Å: Chain D: A.11, C.12, G.13, G.15, K.16, S.17, F.28, D.30, E.31, P.34, K.117, L.120, P.121, S.145, A.146, K.147 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.13, D:G.15, D:K.16, D:K.16, D:E.31, D:A.146, D:K.147, D:K.147, D:K.147

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.16, S.17 Ligands: GDP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.16, A:S.17 MG.5: 3 residues within 4Å: Chain D: K.16, S.17 Ligands: GDP.4 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:K.16, D:S.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samson, C. et al., A Coiled Coil Module Strategy for High-Resolution Cryo-EM Structures of Small Proteins for Drug Discovery. To Be Published

Release Date

2025-11-12

Peptides

Isoform 2B of GTPase KRas,APH2: AD
Nanobody 26: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
M

C
N

Isoform 2B of GTPase KRas,APH2

Nanobody 26