SMTL ID : 6zvq.1

Complex between SMAD2 MH2 domain and peptide from Ski corepressor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

hetero-3-3-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: Q.160, G.161, F.162, E.163, S.218, P.219, S.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.162, A:E.163, A:E.163, A:S.218, A:S.220 Water bridges: A:A.164 SO4.2: 5 residues within 4Å: Chain A: Q.118, W.182, Q.189, T.190, V.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.118, A:Q.118, A:Q.189, A:V.191 SO4.14: 7 residues within 4Å: Chain C: Q.160, G.161, F.162, E.163, S.218, P.219, S.220 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.162, C:E.163, C:E.163, C:S.218, C:S.220 Water bridges: C:A.164 SO4.15: 5 residues within 4Å: Chain C: Q.118, W.182, Q.189, T.190, V.191 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.118, C:Q.118, C:Q.189, C:V.191 SO4.27: 7 residues within 4Å: Chain E: Q.160, G.161, F.162, E.163, S.218, P.219, S.220 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:F.162, E:E.163, E:S.218, E:S.220 Water bridges: E:A.164 SO4.28: 5 residues within 4Å: Chain E: Q.118, W.182, Q.189, T.190, V.191 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.118, E:Q.118, E:Q.189, E:V.191

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.48, D.64, P.65, R.70, F.71, C.72, L.75 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: S.77, N.78, V.79, R.81, E.86 Chain C: R.175 Ligands: TAR.21 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: S.56, R.97, Y.99, E.108 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: S.66, N.67, S.68 Chain C: S.29 Ligands: TAR.13 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: E.30, P.31, A.32, F.33, W.34, Y.100 Chain B: L.22, G.23 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: G.47, L.75, L.76, S.77 Chain C: A.38, Y.40, R.45, E.199, H.201 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: W.128, T.132, V.133, C.134 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: G.139, C.140, N.141 Ligands: TAR.7 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain C: E.48, D.64, P.65, R.70, F.71, C.72, L.75 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: S.77, N.78, V.79, R.81, E.86 Chain E: R.175 Ligands: TAR.34 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain C: S.56, R.97, Y.99, E.108 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain C: S.66, N.67, S.68 Chain E: S.29 Ligands: TAR.26 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain C: E.30, P.31, A.32, F.33, W.34, Y.100 Chain D: L.22, G.23 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain C: G.47, L.75, L.76, S.77 Chain E: A.38, Y.40, R.45, E.199, H.201 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain C: W.128, T.132, V.133, C.134 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: G.139, C.140, N.141 Ligands: TAR.20 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain E: E.48, D.64, P.65, R.70, F.71, C.72, L.75 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: R.175 Chain E: S.77, N.78, V.79, R.81, E.86 Ligands: TAR.8 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain E: S.56, R.97, Y.99, E.108 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain A: S.29 Chain E: S.66, N.67, S.68 Ligands: TAR.39 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain E: E.30, P.31, A.32, F.33, W.34, Y.100 Chain F: L.22, G.23 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain A: A.38, Y.40, R.45, E.199, H.201 Chain E: G.47, L.75, L.76, S.77 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain E: W.128, T.132, V.133, C.134 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain E: G.139, C.140, N.141 Ligands: TAR.33 Ligand excluded by PLIP

9 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.7: 3 residues within 4Å: Chain A: N.141, L.142 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.143 TAR.8: 11 residues within 4Å: Chain A: T.169, R.170, T.173, R.175 Chain E: G.74, L.75, L.76, S.77, R.81, R.89 Ligands: GOL.30 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:T.169, A:T.169, A:T.173, E:L.75 Water bridges: A:R.170, E:R.89, E:R.89 Salt bridges: A:R.175, E:R.81, E:R.89 TAR.13: 5 residues within 4Å: Chain A: F.33, T.49, F.50, H.51 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.51 Salt bridges: A:H.51 TAR.20: 3 residues within 4Å: Chain C: N.141, L.142 Ligands: GOL.25 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.143 TAR.21: 11 residues within 4Å: Chain A: G.74, L.75, L.76, S.77, R.81, R.89 Chain C: T.169, R.170, T.173, R.175 Ligands: GOL.4 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:L.75, C:T.169, C:T.169, C:T.173 Water bridges: A:R.89, A:R.89, C:R.170 Salt bridges: A:R.81, A:R.89, C:R.175 TAR.26: 5 residues within 4Å: Chain C: F.33, T.49, F.50, H.51 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.51 Salt bridges: C:H.51 TAR.33: 3 residues within 4Å: Chain E: N.141, L.142 Ligands: GOL.38 1 PLIP interactions: 1 interactions with chain E Water bridges: E:K.143 TAR.34: 11 residues within 4Å: Chain C: G.74, L.75, L.76, S.77, R.81, R.89 Chain E: T.169, R.170, T.173, R.175 Ligands: GOL.17 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:T.169, E:T.169, C:L.75 Water bridges: E:R.170, C:R.89, C:R.89 Salt bridges: E:R.175, C:R.81, C:R.89 TAR.39: 5 residues within 4Å: Chain E: F.33, T.49, F.50, H.51 Ligands: GOL.32 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.51 Salt bridges: E:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gori, I. et al., Mutations in SKI in Shprintzen-Goldberg syndrome lead to attenuated TGF-beta responses through SKI stabilization. Elife (2021)

Release Date

2021-06-09

Peptides

Mothers against decapentaplegic homolog 2: ACE
Ski oncogene: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Mothers against decapentaplegic homolog 2

Ski oncogene

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