SMTL ID : 6kyk.2 (1 other biounit)

Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-1-2-mer

Ligands

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

GNP.1: 25 residues within 4Å: Chain B: G.15, G.16, V.17, G.18, K.19, S.20, A.21, F.31, V.32, E.33, K.34, Y.35, P.37, T.38, T.61, A.62, G.63, N.119, K.120, D.122, L.123, S.150, A.151, K.152 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.16, B:V.17, B:G.18, B:K.19, B:K.19, B:K.19, B:S.20, B:A.21, B:V.32, B:Y.35, B:T.38, B:T.38, B:T.61, B:G.63, B:T.64, B:N.119, B:K.120, B:K.120, B:S.150, B:A.151, B:K.152 Water bridges: B:T.38, B:T.38 Salt bridges: B:D.122 pi-Stacking: B:F.31 GNP.3: 24 residues within 4Å: Chain C: G.15, G.16, V.17, G.18, K.19, S.20, A.21, F.31, V.32, E.33, Y.35, P.37, T.38, A.62, G.63, T.64, N.119, K.120, D.122, L.123, S.150, A.151, K.152 Ligands: MG.4 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:G.16, C:V.17, C:G.18, C:K.19, C:K.19, C:K.19, C:S.20, C:S.20, C:A.21, C:V.32, C:E.33, C:Y.35, C:T.38, C:T.38, C:T.38, C:T.38, C:G.63, C:T.64, C:K.120, C:K.120, C:S.150, C:A.151, C:K.152 Salt bridges: C:D.122 pi-Stacking: C:F.31, C:F.31

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: S.20, T.38, D.60 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.20, B:T.38, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain C: S.20, D.36, T.38, D.60 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.20, C:T.38, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Q. et al., Shank3 Binds to and Stabilizes the Active Form of Rap1 and HRas GTPases via Its NTD-ANK Tandem with Distinct Mechanisms. Structure (2020)

Release Date

2019-12-04

Peptides

SH3 and multiple ankyrin repeat domains protein 3: A
Ras-related protein Rap-1b: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
F

SH3 and multiple ankyrin repeat domains protein 3

Ras-related protein Rap-1b

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