SMTL ID : 6yk0.1 (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 PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 12 residues within 4Å: Chain A: S.14, V.16, V.21, V.43, F.45, N.47, H.48, T.49, W.54, V.58, Y.86, R.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.47, A:T.49 PG4.4: 7 residues within 4Å: Chain A: E.6, R.8, K.78, Y.79, D.80, N.107 Chain B: R.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.107

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

AGS.2: 23 residues within 4Å: Chain A: D.115, P.116, V.117, D.120, T.150, P.151, 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.115, A:D.115, A:D.120, A:D.120, A:N.152, A:T.188, A:S.189, A:V.228, A:V.228, A:T.235 AGS.8: 26 residues within 4Å: Chain B: D.115, 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, V.231, F.232, T.235, G.236, F.239, V.262, M.265, Q.266, L.269 Ligands: EDO.16 7 PLIP interactions: 7 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

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

EDO.3: 7 residues within 4Å: Chain A: E.6, C.7, L.33, G.34, F.35, H.248, K.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.248, A:K.249 EDO.6: 4 residues within 4Å: Chain A: G.161, R.162, K.163, H.165 No protein-ligand interaction detected (PLIP) EDO.7: 9 residues within 4Å: Chain A: H.15, N.41, Q.44 Chain B: H.15, N.41, S.42, V.43, Q.44, L.59 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.41, A:Q.44, B:N.41, B:N.41 EDO.9: 5 residues within 4Å: Chain B: H.267, Q.270, R.271, R.274, D.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.267, B:R.271, B:R.274 EDO.11: 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 EDO.12: 6 residues within 4Å: Chain B: L.135, E.157, L.158, G.161, R.162, K.163 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain B: K.104, S.108, R.109, L.110, V.111, D.147 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: D.304, P.305, E.306 No protein-ligand interaction detected (PLIP) EDO.15: 9 residues within 4Å: Chain B: S.42, V.43, V.58, L.59, Y.86, T.87, R.88, D.89, F.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.59, B:T.87 EDO.16: 5 residues within 4Å: Chain B: D.120, S.189, L.201, K.227 Ligands: AGS.8 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: H.65, Y.68, E.69, K.72, M.95, D.98, I.99, E.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.98 GOL.10: 5 residues within 4Å: Chain B: C.7, L.33, G.34, F.35, H.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.7, B:L.33, B:H.248

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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