SMTL ID : 8vmg.1 (1 other biounit)

Crystal structure of GSK-3 26-383 bound to Axin 383-435

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 18 residues within 4Å: Chain A: N.39, V.45, A.58, K.60, V.85, L.107, D.108, Y.109, V.110, T.113, Q.160, N.161, L.163, C.174, D.175 Ligands: EDO.5, NO3.29, MG.36 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.108, A:V.110, A:D.175 Water bridges: A:K.60, A:K.60, A:T.113, A:T.113, A:N.161, A:D.175, A:D.175, A:D.175 Salt bridges: A:K.60, A:K.60

20 x EDO: 1,2-ETHANEDIOL

EDO.2: 7 residues within 4Å: Chain A: Y.115, A.118, R.119, S.122, E.224, G.228, Q.229 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: P.251, T.252, R.253, I.256, F.266, K.267, F.268, Q.270 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: H.81, C.82, R.142, N.336, T.338, E.341 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: I.37, Y.109, V.110, P.111, E.112, T.113, R.116 Ligands: ADP.1 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: K.278, P.282 Ligands: EDO.22 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.129, V.130, I.131 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: S.194, R.195, Y.196 Ligands: NO3.27, SO4.34 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: R.294, L.304, E.308, A.311, H.312 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: P.187, N.188, V.189, T.207 Ligands: EDO.23, SO4.31 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: P.275, W.276 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain A: M.1, Y.31, T.34, Y.46, I.59, K.61, F.91, S.93, N.104 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: H.148, S.211, S.212, V.215, P.300, R.303, L.304, T.305, P.306 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: T.277, K.278 Ligands: EDO.6 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: N.188, V.189, S.190, Y.191, G.205, T.207 Ligands: EDO.16 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: T.338, T.339 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: H.81, C.82, I.84, V.85, R.86, D.108, K.172 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain A: Q.270, I.271, K.272 Chain B: Q.25, R.28, E.29 Ligand excluded by PLIP EDO.43: 1 residues within 4Å: Chain B: T.27 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain A: F.266 Chain B: Q.11, A.14, E.15, I.18 Ligand excluded by PLIP EDO.45: 1 residues within 4Å: Chain B: R.37 Ligand excluded by PLIP

8 x NO3: NITRATE ION

NO3.7: 3 residues within 4Å: Chain A: R.281, P.282, R.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.281, A:R.283 NO3.8: 5 residues within 4Å: Chain A: P.332, A.333, L.334, F.335, N.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.334, A:F.335, A:N.336 NO3.9: 3 residues within 4Å: Chain A: V.16, T.18, F.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.16, A:T.18 NO3.12: 5 residues within 4Å: Chain A: Y.191, I.192, C.193 Ligands: SO4.33, SO4.34 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.193, A:C.193 NO3.20: 5 residues within 4Å: Chain A: Q.64, D.65, F.68, K.69, N.70 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.64, A:Q.64, A:D.65, A:K.69, A:N.70 Water bridges: A:E.72 NO3.27: 3 residues within 4Å: Chain A: R.195, D.235 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.195, A:R.195, A:D.235 NO3.28: 2 residues within 4Å: Chain A: G.40, S.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.41 NO3.29: 8 residues within 4Å: Chain A: N.39, G.40, G.43, V.44, V.45, K.60, V.62 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.39

4 x GOL: GLYCEROL

GOL.10: 2 residues within 4Å: Chain A: R.119, R.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.119 GOL.14: 5 residues within 4Å: Chain A: L.50, R.86, R.88, Y.89 Ligands: GOL.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.86, A:R.88, A:Y.89, A:Y.89 GOL.19: 8 residues within 4Å: Chain A: E.28, V.29, S.30, L.50, D.52, S.53, Y.89 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.30, A:D.52, A:S.53, A:S.53 GOL.25: 6 residues within 4Å: Chain A: Y.191, R.198, S.236, G.237, V.238 Ligands: SO4.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.191, A:Y.191, A:G.237, A:V.238 Water bridges: A:R.198

7 x SO4: SULFATE ION

SO4.30: 3 residues within 4Å: Chain A: K.246, H.274 Chain B: R.28 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.28, A:K.246, A:H.274 Hydrogen bonds: A:K.246 SO4.31: 7 residues within 4Å: Chain A: K.69, R.71, R.155, K.180, N.188, V.189 Ligands: EDO.16 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.189 Water bridges: A:R.71, A:K.180, A:K.180 Salt bridges: A:K.69, A:R.71, A:R.155, A:K.180 SO4.32: 1 residues within 4Å: Chain A: R.71 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.71 SO4.33: 7 residues within 4Å: Chain A: Y.191, R.195, R.198, S.236, G.237 Ligands: NO3.12, GOL.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.191 Salt bridges: A:R.195, A:R.198 SO4.34: 4 residues within 4Å: Chain A: K.158, S.194 Ligands: NO3.12, EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.194 Water bridges: A:K.158, A:S.194, A:R.195 Salt bridges: A:K.158 SO4.35: 4 residues within 4Å: Chain A: Y.121, Y.132, Y.136, P.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.136, A:Y.136 SO4.46: 4 residues within 4Å: Chain A: D.235, S.236, D.239 Chain B: R.20 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.20 Hydrogen bonds: A:S.236

1 x MG: MAGNESIUM ION

MG.36: 3 residues within 4Å: Chain A: N.161, D.175 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, H2O.3

7 x CL: CHLORIDE ION

CL.37: 2 residues within 4Å: Chain A: Q.270 Chain B: Q.25 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain A: K.158, Q.160 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain A: R.184 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain A: R.253, R.257 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain A: Q.255, E.297, Y.298 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain B: E.35 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain B: K.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enos, M.D. et al., Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3 beta. Sci.Signal. (2024)

Release Date

2024-08-28

Peptides

Glycogen synthase kinase-3 beta: A
Axin-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Glycogen synthase kinase-3 beta

Axin-1

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