SMTL ID : 7c7j.1 (1 other biounit)

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 27 residues within 4Å: Chain A: S.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, E.30, K.31, Y.32, P.34, T.35, D.57, T.58, A.59, G.60, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:S.17, A:A.18, A:V.29, A:T.35, A:T.35, A:T.58, A:G.60, A:N.116, A:K.117, A:K.117, A:S.147, A:A.148, A:K.149 Salt bridges: A:K.16, A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: N.155, E.156 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.156, A:E.156, H2O.1, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.17, D.33, T.35 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.17, A:T.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X.L. et al., Mechanistic Insights into the Interactions of Ras Subfamily GTPases with the SPN Domain of Autism-associated SHANK3. Chin.J.Chem. (2020)

Release Date

2021-05-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Ras-related protein Rap-1b

SH3 and multiple ankyrin repeat domains protein 3

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