SMTL ID : 6yk1.1 (1 other biounit)

Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S and artesunate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: P.193 No protein-ligand interaction detected (PLIP) GOL.16: 1 residues within 4Å: Chain B: K.121 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain B: C.7, L.33, G.34, F.35, H.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.248

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 4 residues within 4Å: Chain A: G.161, R.162, K.163 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.163

1 x D95: Artesunate(Non-covalent)

D95.3: 18 residues within 4Å: Chain A: S.14, V.16, V.21, S.42, V.43, F.45, N.47, H.48, T.49, W.54, V.58, K.60, Y.86, T.87, R.88, D.89 Ligands: EDO.8, EDO.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.16, A:V.43, A:F.45, A:F.45, A:F.45, A:T.49, A:W.54, A:V.58, A:R.88 Salt bridges: A:K.60, A:R.88, A:R.88

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.4: 25 residues within 4Å: Chain A: D.115, P.116, V.117, D.120, Y.129, T.150, P.151, N.152, E.155, T.188, S.189, L.201, M.225, R.226, K.227, V.228, A.230, F.232, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.115, A:D.120, A:N.152, A:T.188, A:S.189, A:V.228, A:V.228, A:T.235, A:G.236 AGS.18: 21 residues within 4Å: Chain B: D.115, V.117, D.120, T.150, N.152, E.155, T.188, S.189, M.225, R.226, K.227, V.228, A.230, F.232, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.115, B:D.115, B:D.120, B:N.152, B:T.188, B:S.189, B:K.227, B:V.228, B:V.228, B:T.235, B:G.236, B:Q.266 Water bridges: B:T.235

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

EDO.5: 1 residues within 4Å: Ligands: PG4.2 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: N.77, K.78, Y.79, L.103, Q.106, N.107, L.110 Ligands: EDO.13 Ligand excluded by PLIP EDO.7: 12 residues within 4Å: Chain A: Q.13, A.26, L.83, T.84, G.85, Y.86, D.115, V.117, G.236, D.237, A.240, A.241 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: S.14, V.21, H.48, T.49, G.50, Y.86, V.233 Ligands: D95.3 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: K.121, G.126 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: H.65, Y.68, E.69, K.72, M.95, D.98, I.99, E.102 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.32, L.33, G.34, K.249, E.303 Chain B: K.299 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: F.45, W.54, K.55, G.56, Q.57, V.58 Ligands: D95.3 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: K.78, Y.79, D.80, N.107 Ligands: EDO.6 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: E.6, C.7, L.33, G.34, F.35, H.248, K.249 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: V.111, D.147, I.148, D.183, T.184 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: N.74 Chain B: Y.51, A.52, S.287, P.288, A.289 Ligand excluded by PLIP EDO.20: 11 residues within 4Å: Chain B: S.14, V.16, V.21, V.43, F.45, N.47, H.48, T.49, Y.86, V.233 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain B: S.14, S.42, V.43, F.45, T.49, Y.86, T.87, R.88 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain A: H.15, N.41, V.43, Q.44, L.59 Chain B: H.15, N.41, Q.44, L.59 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: H.65, Y.68, E.69, M.95, D.98, I.99, E.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2021-04-14

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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