SMTL ID : 3fhy.1

Crystal structure of D235N mutant of human pyridoxal kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.118 Ligands: ATP.3, SO4.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, H2O.1, H2O.4 MG.11: 4 residues within 4Å: Chain B: D.118, S.187 Ligands: ATP.13, SO4.19 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.118, H2O.8, H2O.8

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 7 residues within 4Å: Chain A: D.113, T.148, P.149, N.150, E.153, T.186 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.113, A:T.186 Water bridges: A:T.148 NA.12: 7 residues within 4Å: Chain B: D.113, T.148, P.149, N.150, E.153, T.186 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.113, B:T.148

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 22 residues within 4Å: Chain A: D.113, D.118, Y.127, N.150, E.153, T.186, S.187, V.201, R.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.263, L.267 Ligands: MG.1, NA.2, SO4.7, SO4.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.127, A:N.150, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226, A:G.234 Water bridges: A:Y.127, A:Y.127, A:T.233, A:T.233 ATP.13: 24 residues within 4Å: Chain B: D.113, G.117, D.118, Y.127, N.150, E.153, T.186, S.187, L.199, V.201, I.223, R.224, K.225, V.226, A.228, T.233, G.234, F.237, L.263, L.267 Ligands: MG.11, NA.12, SO4.19, SO4.20 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.127, B:Y.127, B:N.150, B:T.186, B:T.186, B:S.187, B:V.226, B:V.226, B:T.233 Water bridges: B:T.148, B:F.230

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: C.5, L.31, G.32, F.33, K.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.5 Salt bridges: A:H.246, A:K.247 SO4.5: 4 residues within 4Å: Chain A: E.155, L.156, G.159, K.161 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain A: A.144, D.145, G.179, D.181 Ligands: MPD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181 SO4.7: 3 residues within 4Å: Chain A: D.118 Ligands: MG.1, ATP.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.187, A:S.187 SO4.8: 6 residues within 4Å: Chain A: V.231, G.232, T.233, G.234, N.235 Ligands: ATP.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.232, A:G.234, A:N.235, A:N.235 Water bridges: A:T.233 SO4.14: 3 residues within 4Å: Chain B: E.155, R.160, K.161 No protein-ligand interaction detected (PLIP) SO4.15: 4 residues within 4Å: Chain B: C.5, L.31, G.32, H.246 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.34 Salt bridges: B:H.246 SO4.16: 5 residues within 4Å: Chain A: V.56, E.61 Chain B: Q.55, V.56, E.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.61 Water bridges: A:Q.55 SO4.17: 2 residues within 4Å: Chain B: R.70, E.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63 Salt bridges: B:R.70 SO4.18: 4 residues within 4Å: Chain B: P.142, D.145, G.179, D.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.145 Water bridges: B:G.179 SO4.19: 5 residues within 4Å: Chain B: D.118, S.187, L.199 Ligands: MG.11, ATP.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.118, B:S.187 SO4.20: 7 residues within 4Å: Chain B: V.231, G.232, T.233, G.234, N.235 Ligands: ATP.13, MPD.25 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.232, B:T.233, B:T.233, B:G.234, B:N.235, B:N.235

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 4 residues within 4Å: Chain A: D.181, R.206, R.208 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.206, A:R.208 Hydrogen bonds: A:D.181 MPD.10: 6 residues within 4Å: Chain A: Q.63, Y.66, R.70, M.93, D.96, E.100 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.66, A:D.96, A:E.100 Hydrogen bonds: A:Q.63, A:R.70 MPD.21: 5 residues within 4Å: Chain B: D.181, R.206, R.207, R.208, V.214 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.214 Hydrogen bonds: B:D.181, B:R.206 MPD.22: 2 residues within 4Å: Chain B: V.311, L.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.312 MPD.23: 4 residues within 4Å: Chain B: H.248, P.249, N.250, N.251 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.249, B:N.250 Hydrogen bonds: B:N.250, B:N.251 MPD.24: 3 residues within 4Å: Chain B: G.124, E.130, F.152 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.152 Hydrogen bonds: B:E.130, B:E.130 MPD.25: 9 residues within 4Å: Chain B: S.12, V.19, F.43, H.46, T.47, Y.84, V.231, N.235 Ligands: SO4.20 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.19, B:F.43, B:Y.84, B:V.231 Hydrogen bonds: B:G.20, B:T.47, B:T.47, B:N.235 Water bridges: B:Y.84, B:N.235 MPD.26: 3 residues within 4Å: Chain B: P.191, P.193, R.220 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.193 Water bridges: B:Q.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandhi, A.K. et al., Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem.Biophys.Res.Commun. (2009)

Release Date

2008-12-23

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase