SMTL ID : 6yk0.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

AGS.1: 25 residues within 4Å: Chain A: D.115, V.117, G.119, D.120, Y.129, N.152, E.155, T.188, S.189, L.201, M.225, R.226, K.227, V.228, A.230, V.231, F.232, T.235, G.236, D.237, F.239, V.262, M.265, Q.266, L.269 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.152, A:T.188, A:S.189, A:S.189, A:V.228, A:V.228, A:T.235 AGS.9: 24 residues within 4Å: Chain B: D.115, V.117, D.120, T.150, P.151, N.152, E.155, T.188, S.189, L.201, M.225, R.226, K.227, V.228, A.230, V.231, F.232, T.235, G.236, D.237, F.239, M.265, Q.266, L.269 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.115, B:D.115, B:N.152, B:T.188, B:S.189, B:V.228, B:V.228, B:T.235, B:G.236

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

EDO.2: 7 residues within 4Å: Chain A: K.104, P.144, V.145, A.146, D.147, G.181, P.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.181 EDO.4: 8 residues within 4Å: Chain A: S.14, V.21, V.43, F.45, H.48, T.49, Y.86, V.233 No protein-ligand interaction detected (PLIP) EDO.5: 7 residues within 4Å: Chain A: E.6, C.7, L.33, G.34, F.35, H.248 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.6, A:E.6 EDO.6: 8 residues within 4Å: Chain A: L.33, F.35, A.245, W.246, H.248, K.249, E.303 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.248 EDO.7: 5 residues within 4Å: Chain A: R.88, Y.129, V.130, P.131, Q.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:Y.129, A:Q.132 EDO.8: 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 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.41, B:N.41 EDO.10: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.65, Y.68, E.69, M.95, D.98, I.99, E.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.65

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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