SMTL ID : 7c7i.1

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: S.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, D.33, T.35, D.57, T.58, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:S.11, A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:V.29, A:T.35, A:T.35, A:T.35, A:T.58, A:N.116, A:K.117, A:K.117, A:A.148, A:K.149 Water bridges: A:K.16, A:K.16 Salt bridges: A:K.16, A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28 GTP.4: 25 residues within 4Å: Chain B: S.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, D.33, T.35, D.57, T.58, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.5 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:S.17, B:A.18, B:V.29, B:T.35, B:T.35, B:T.35, B:N.116, B:K.117, B:K.117, B:A.148, B:K.149 Water bridges: B:D.33, B:G.60 Salt bridges: B:K.16, B:K.16, B:D.119 pi-Stacking: B:F.28, B:F.28

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: N.155, E.156 Chain B: N.155, E.156 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.156, B:E.156, B:E.156, H2O.2, H2O.4

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.17, Y.32, D.33, T.35 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.33 MG.5: 5 residues within 4Å: Chain B: S.17, Y.32, D.33, T.35 Ligands: GTP.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.33, H2O.4

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: AB
SH3 and multiple ankyrin repeat domains protein 3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ras-related protein Rap-1b

SH3 and multiple ankyrin repeat domains protein 3

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