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

Crystal structure of mouse pyridoxal kinase in apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

PG4.1: 10 residues within 4Å: Chain A: S.14, V.21, V.43, F.45, H.48, T.49, W.54, V.58, Y.86, R.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.14, A:R.88 Water bridges: A:T.49 PG4.5: 15 residues within 4Å: Chain A: T.188, S.189, L.201, M.225, R.226, K.227, V.228, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.228, A:V.228, A:Q.266

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: E.6, C.7, L.33, G.34, F.35, H.248, K.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.7 GOL.6: 7 residues within 4Å: Chain A: Q.57, V.58, L.59, K.60, E.63 Chain B: K.60, E.63 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.63, A:V.58, A:K.60, A:E.63 Water bridges: B:K.60, B:K.60 GOL.10: 6 residues within 4Å: Chain B: E.6, C.7, L.33, G.34, F.35, H.248 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.6, B:E.6, B:L.33, B:H.248 Water bridges: B:L.33

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

EDO.3: 2 residues within 4Å: Chain A: R.162, K.163 No protein-ligand interaction detected (PLIP) EDO.4: 11 residues within 4Å: Chain A: D.115, P.116, V.117, Y.129, T.150, P.151, N.152, E.155, T.188, G.236 Ligands: PG4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.129, A:Y.129, A:T.150, A:N.152, A:T.188 EDO.7: 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:E.69, A:K.72 EDO.8: 9 residues within 4Å: Chain A: H.15, N.41, V.43, Q.44, L.59 Chain B: H.15, N.41, V.43, Q.44 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.41, B:Q.44, A:N.41 EDO.9: 6 residues within 4Å: Chain A: R.18 Chain B: E.6, C.7, R.8, E.36, K.78 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.18 Hydrogen bonds: B:R.8, B:R.8, B:K.78 EDO.11: 10 residues within 4Å: Chain B: D.115, P.116, V.117, Y.129, T.150, P.151, N.152, E.155, T.188, G.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.129, B:T.150, B:N.152, B:T.188 EDO.12: 6 residues within 4Å: Chain B: H.65, Y.68, M.95, D.98, I.99, E.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.65, B:E.102 EDO.13: 9 residues within 4Å: Chain B: S.14, V.16, V.21, V.43, F.45, H.48, T.49, Y.86, V.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.49

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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