SMTL ID : 2yxt.1 (1 other biounit)

Human Pyridoxal Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: D.113, T.148, E.153, T.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.113, A:T.186 NA.8: 3 residues within 4Å: Chain B: T.148, E.153, T.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.153

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: Q.63, R.70, M.93, I.97, E.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.63 Water bridges: A:E.100 Salt bridges: A:R.70 PO4.9: 6 residues within 4Å: Chain B: C.5, L.31, G.32, F.33, H.246, K.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.31, B:L.31 Salt bridges: B:H.246, B:K.247 PO4.10: 7 residues within 4Å: Chain B: Y.198, D.222, I.223, R.224, H.264, V.306 Ligands: MPD.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.224, B:V.306 Salt bridges: B:H.264 PO4.11: 4 residues within 4Å: Chain B: D.145, G.179, D.181 Ligands: MPD.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.179, B:G.179 Water bridges: B:D.145, B:G.179 PO4.12: 4 residues within 4Å: Chain B: E.155, G.159, R.160, K.161 No protein-ligand interaction detected (PLIP) PO4.13: 6 residues within 4Å: Chain B: Q.63, Y.66, R.70, D.96, I.97, E.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:D.96 Salt bridges: B:R.70

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

MPD.3: 6 residues within 4Å: Chain A: S.12, V.14, V.19, F.43, T.47, Y.84 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.14, A:V.19, A:F.43, A:T.47 Hydrogen bonds: A:S.12, A:S.12 Water bridges: A:S.12 MPD.4: 7 residues within 4Å: Chain A: T.186, S.187, I.223, T.233, G.234, F.237, L.263 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.237, A:L.263 Hydrogen bonds: A:T.233 MPD.5: 6 residues within 4Å: Chain A: R.224, K.225, V.226, H.264, L.267, Q.268 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.226, A:L.267 Hydrogen bonds: A:H.264, A:Q.268 MPD.6: 5 residues within 4Å: Chain A: L.31, G.32, F.33, H.246, K.247 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.33 Hydrogen bonds: A:K.247 MPD.7: 5 residues within 4Å: Chain A: D.222, I.223, R.224, V.306, V.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.224 Hydrogen bonds: A:R.224, A:V.306 MPD.14: 6 residues within 4Å: Chain B: T.186, L.199, T.233, G.234, F.237 Ligands: MPD.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.237 Hydrogen bonds: B:T.233 Water bridges: B:T.233 MPD.15: 7 residues within 4Å: Chain B: I.223, R.224, H.264, L.267, Q.268 Ligands: PO4.10, MPD.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.224, B:L.267 Hydrogen bonds: B:H.264 MPD.16: 5 residues within 4Å: Chain B: D.181, R.206, R.208, V.214 Ligands: PO4.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.206, B:V.214 Hydrogen bonds: B:D.181 MPD.17: 7 residues within 4Å: Chain B: S.12, V.19, H.46, T.47, V.231 Ligands: MPD.18, MPD.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.19, B:T.47, B:V.231 Hydrogen bonds: B:S.12, B:S.12, B:T.47, B:T.47 Water bridges: B:S.12 MPD.18: 6 residues within 4Å: Chain B: F.43, V.56, Y.84, R.86 Ligands: MPD.17, MPD.21 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.43, B:F.43, B:V.56 Hydrogen bonds: B:R.86, B:R.86 MPD.19: 3 residues within 4Å: Chain B: M.126, E.130, L.156 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.130, B:L.156 Water bridges: B:G.124 MPD.20: 4 residues within 4Å: Chain B: D.173, H.176, S.177, R.206 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.176 MPD.21: 5 residues within 4Å: Chain B: T.47, Y.84, Y.127 Ligands: MPD.17, MPD.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.84, B:Y.127 Hydrogen bonds: B:T.47 MPD.22: 5 residues within 4Å: Chain B: V.109, I.146, Q.205, T.245, P.249 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.146 Hydrogen bonds: B:T.245 Water bridges: B:Y.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Musayev, F.N. et al., Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Protein Sci. (2007)

Release Date

2008-03-11

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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