SMTL ID : 8be9.1

Crystal structure of SOS1-HRas-peptidomimetic5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- 7XC- HIS- PRO- TRP- SER- VAL- ALA- XSN: SOS1-HRas-peptidomimetic5(Non-covalent)

LYS-7XC-HIS-PRO-TRP-SER-VAL-ALA-XSN.1: 13 residues within 4Å: Chain B: M.336, N.337, Y.342, D.345, F.348, K.356, K.357, L.359, E.360, H.363, E.364, E.367, D.368 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:M.336, B:Y.342, B:Y.342, B:F.348, B:L.359, B:H.363 Hydrogen bonds: B:Y.342, B:K.356, B:E.360, B:E.367, B:E.367 Water bridges: B:E.360, B:E.367, B:D.368 Salt bridges: B:E.364, B:E.367

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

CL.2: 1 residues within 4Å: Chain A: D.53 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: Q.42 Ligand excluded by PLIP

14 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 6 residues within 4Å: Chain A: K.25, R.93, T.94, G.95, E.96, K.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.124, A:K.124 FMT.6: 5 residues within 4Å: Chain A: F.110, E.111, I.113, H.114, L.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.114, A:Y.157 FMT.7: 4 residues within 4Å: Chain A: R.88, D.112, Q.115, Y.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.112, A:Y.116 FMT.8: 4 residues within 4Å: Chain A: E.118, K.121, D.127 Ligands: FMT.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.121 FMT.9: 6 residues within 4Å: Chain A: K.121, R.122, D.125, S.126, D.127 Ligands: FMT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.125 FMT.10: 7 residues within 4Å: Chain A: L.76, D.77, T.78, Q.81 Chain B: H.369, Y.370, T.393 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.81 Water bridges: A:D.77 FMT.11: 3 residues within 4Å: Chain B: R.284, N.288, M.455 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.288 FMT.12: 4 residues within 4Å: Chain B: P.79, V.82, N.149, H.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.149, B:H.153 FMT.13: 1 residues within 4Å: Chain B: R.484 No protein-ligand interaction detected (PLIP) FMT.14: 4 residues within 4Å: Chain B: S.458, E.462, F.463, Y.466 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.458, B:E.462 FMT.15: 5 residues within 4Å: Chain B: R.90, S.91, F.92, C.93, K.94 No protein-ligand interaction detected (PLIP) FMT.16: 4 residues within 4Å: Chain B: E.349, Q.350, I.351, P.352 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.349 FMT.17: 5 residues within 4Å: Chain B: H.285, N.288, F.449, E.450, L.452 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.285, B:N.288, B:F.449 FMT.18: 4 residues within 4Å: Chain B: K.487, K.488, Y.489, S.490 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Holsbeeck, K. et al., Nanobody Loop Mimetics Enhance Son of Sevenless 1-Catalyzed Nucleotide Exchange on RAS. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-04-26

Peptides

GTPase HRas: A
Son of sevenless homolog 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
S

GTPase HRas

Son of sevenless homolog 1

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