SMTL ID : 6oid.1

Redox Regulation of FN3K from Arabidopsis thaliana

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: N.54, A.56, F.67, K.69, P.98, M.115, E.116, F.117, I.118, F.120, D.239 Chain B: F.296, G.297, S.298 Ligands: EDO.15, DMS.16 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:F.296, B:S.298, A:N.54, A:E.116, A:I.118 Water bridges: A:K.69 Salt bridges: A:K.69, A:K.69 pi-Stacking: A:F.67, A:F.67 ADP.17: 15 residues within 4Å: Chain A: F.296, G.297, S.298 Chain B: N.54, A.56, F.67, K.69, P.98, M.115, E.116, F.117, I.118, F.120, D.239 Ligands: EDO.12 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.54, B:E.116, B:I.118, B:D.239, A:S.298 Water bridges: B:K.69 Salt bridges: B:K.69, B:K.69 pi-Stacking: B:F.67, B:F.67

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

SO4.2: 5 residues within 4Å: Chain A: A.275, G.276, Y.277, E.278, K.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.276, A:G.276, A:Y.277, A:E.278, A:K.279 SO4.3: 5 residues within 4Å: Chain A: R.96, E.116, I.118, D.119, K.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.116, A:D.119 Water bridges: A:K.231 Salt bridges: A:R.96, A:K.231 SO4.4: 4 residues within 4Å: Chain A: A.192, K.196, R.301 Chain B: S.123 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.196, A:R.301 Hydrogen bonds: B:S.123, B:S.123 SO4.5: 2 residues within 4Å: Chain A: R.132, K.133 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.132, A:K.133 SO4.6: 3 residues within 4Å: Chain A: K.182, R.185, Y.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.194 Salt bridges: A:K.182, A:R.185 SO4.7: 4 residues within 4Å: Chain A: H.58 Chain B: K.44, G.46 Ligands: DMS.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.46 Salt bridges: B:K.44, A:H.58 SO4.8: 4 residues within 4Å: Chain A: Y.90, N.99, H.101, E.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.90, A:N.99 Salt bridges: A:H.101 SO4.9: 2 residues within 4Å: Chain A: S.165, S.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.166 SO4.10: 4 residues within 4Å: Chain A: N.126, Q.127, A.128, S.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.127, A:A.128, A:S.262 SO4.18: 5 residues within 4Å: Chain B: A.275, G.276, Y.277, E.278, K.279 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.276, B:Y.277, B:E.278, B:K.279 SO4.19: 4 residues within 4Å: Chain B: R.96, I.118, D.119, K.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.116, B:D.119 Salt bridges: B:R.96, B:K.231 SO4.20: 2 residues within 4Å: Chain B: R.132, K.133 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.132, B:K.133 SO4.21: 5 residues within 4Å: Chain A: S.123 Chain B: A.192, K.196, R.301, M.305 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.196, B:R.301 Hydrogen bonds: A:S.123, A:S.123 SO4.22: 4 residues within 4Å: Chain A: K.44, G.46 Chain B: H.58, Q.60 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.58, A:K.44

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 1 residues within 4Å: Chain A: H.292 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: H.292 Ligand excluded by PLIP

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 8 residues within 4Å: Chain A: F.296, G.297, S.298, G.299 Chain B: G.225, I.227, L.238 Ligands: ADP.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.297, A:G.299, B:I.227 EDO.13: 2 residues within 4Å: Chain A: N.99, H.101 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: G.260, E.261, S.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.261, A:S.262, A:S.262 EDO.15: 9 residues within 4Å: Chain A: S.224, G.225, I.227 Chain B: F.296, G.297, S.298, G.299, Y.300 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.224, B:G.299 EDO.24: 4 residues within 4Å: Chain B: N.126, Q.127, A.128, S.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.127, B:A.128, B:S.262, B:S.262

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.16: 8 residues within 4Å: Chain A: A.56, H.58, F.67, F.117 Chain B: G.46, V.48 Ligands: ADP.1, SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 DMS.25: 5 residues within 4Å: Chain B: R.30, I.42, T.43, K.44, I.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrestha, S. et al., A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. Sci.Signal. (2020)

Release Date

2020-05-20

Peptides

Protein-ribulosamine 3-kinase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein-ribulosamine 3-kinase, chloroplastic