SMTL ID : 6yk1.2 (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

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

EDO.1: 5 residues within 4Å: Chain A: Q.105, Q.106, N.107, S.108, R.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.109 EDO.6: 3 residues within 4Å: Chain A: A.52, H.53, W.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.54 EDO.7: 5 residues within 4Å: Chain A: Q.167, E.168, F.171, R.220, L.314 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: C.7, L.33, G.34, F.35, H.248, K.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.33, A:H.248, A:K.249 EDO.9: 8 residues within 4Å: Chain A: S.42, V.43, V.58, L.59, T.87, R.88, D.89, F.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.59, A:L.59, A:R.88 EDO.10: 7 residues within 4Å: Chain A: N.77, K.78, Y.79, L.103, Q.106, N.107, L.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.79, A:L.103, A:N.107 EDO.11: 8 residues within 4Å: Chain A: H.65, Y.68, E.69, K.72, M.95, D.98, I.99, E.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.65, A:E.102 EDO.12: 9 residues within 4Å: Chain A: N.41, V.43, Q.44, L.59 Chain B: H.15, N.41, V.43, Q.44, L.59 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.41, B:N.41, B:Q.44 EDO.14: 6 residues within 4Å: Chain B: E.6, C.7, L.33, G.34, F.35, H.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.33 EDO.15: 10 residues within 4Å: Chain B: S.14, V.16, V.21, V.43, F.45, H.48, T.49, G.50, Y.86, V.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:T.49, B:T.49

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: K.121 No protein-ligand interaction detected (PLIP) GOL.3: 8 residues within 4Å: Chain A: S.14, V.16, V.21, V.43, F.45, H.48, T.49, Y.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:T.49 Water bridges: A:T.49 GOL.4: 8 residues within 4Å: Chain A: K.104, P.144, V.145, A.146, D.147, G.181, P.182, D.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.144, A:G.181

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

AGS.5: 24 residues within 4Å: Chain A: D.115, V.117, G.119, D.120, Y.129, T.150, N.152, E.155, T.188, S.189, M.225, R.226, K.227, V.228, A.230, V.231, F.232, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 11 PLIP interactions: 11 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 Water bridges: A:F.232, A:F.232 AGS.13: 26 residues within 4Å: Chain B: D.115, V.117, M.118, G.119, D.120, Y.129, T.150, P.151, N.152, E.155, T.188, S.189, M.225, R.226, K.227, V.228, A.230, V.231, F.232, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.115, B:Y.129, B:N.152, B:E.155, B:T.188, B:T.188, B:S.189, B:V.228, B:V.228, B:T.235

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
C

B
D

Pyridoxal kinase

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