SMTL ID : 3keu.1

Crystal Structure of Human PL Kinase with bound PLP and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.118 Ligands: ATP.4, MPD.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, H2O.4, H2O.4 MG.2: 4 residues within 4Å: Chain A: V.115, D.235 Ligands: ATP.4, PLP.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.235, PLP.5 MG.12: 4 residues within 4Å: Chain B: D.118, S.187 Ligands: ATP.15, MPD.19 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.118, H2O.11, H2O.11 MG.13: 4 residues within 4Å: Chain B: V.115, D.235 Ligands: ATP.15, PLP.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.235

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

NA.3: 6 residues within 4Å: Chain A: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.186, A:T.186 Water bridges: A:T.148 NA.14: 6 residues within 4Å: Chain B: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.15 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.4: 26 residues within 4Å: Chain A: D.113, V.115, D.118, Y.127, T.148, N.150, E.153, T.186, S.187, L.199, 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, MG.2, NA.3, PLP.5, MPD.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.150, A:E.153, A:E.153, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226, A:G.234 Water bridges: A:T.148, A:H.264 ATP.15: 24 residues within 4Å: Chain B: D.113, D.118, Y.127, T.148, 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, L.263, L.267 Ligands: MG.12, MG.13, NA.14, PLP.17, MPD.19 10 PLIP interactions: 10 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

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.5: 14 residues within 4Å: Chain A: S.12, V.19, G.20, T.47, Y.84, F.230, V.231, G.232, T.233, G.234, D.235 Ligands: MG.2, ATP.4, MPD.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.19, A:Y.84, A:V.231 Hydrogen bonds: A:S.12, A:G.232, A:G.234, A:D.235 Water bridges: A:S.12 PLP.17: 14 residues within 4Å: Chain B: S.12, V.19, G.20, T.47, Y.84, F.230, V.231, G.232, T.233, G.234, D.235 Ligands: MG.13, ATP.15, MPD.16 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.19, B:Y.84, B:V.231 Hydrogen bonds: B:S.12, B:G.20, B:G.232, B:T.233, B:T.233, B:G.234, B:D.235, B:D.235 Water bridges: B:S.12

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

MPD.6: 8 residues within 4Å: Chain A: S.12, V.19, G.20, H.46, T.47, Y.84, D.235 Ligands: PLP.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.19, A:Y.84 Hydrogen bonds: A:S.12, A:G.20, A:T.47 Water bridges: A:S.12, A:Y.84 MPD.7: 4 residues within 4Å: Chain A: D.118, L.199 Ligands: MG.1, ATP.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.199 Water bridges: A:D.118 MPD.8: 4 residues within 4Å: Chain A: E.4, K.76, D.78, N.105 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.105 MPD.16: 11 residues within 4Å: Chain B: S.12, V.14, V.19, F.43, N.45, H.46, T.47, Y.84, V.231, D.235 Ligands: PLP.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.14, B:V.19, B:F.43, B:Y.84, B:V.231 Hydrogen bonds: B:S.12, B:S.12, B:T.47 MPD.18: 5 residues within 4Å: Chain B: D.181, R.206, R.207, R.208, V.214 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.214 Hydrogen bonds: B:D.181 MPD.19: 6 residues within 4Å: Chain B: D.118, L.199, K.225, V.229 Ligands: MG.12, ATP.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.199, B:K.225, B:V.229 Hydrogen bonds: B:D.118 Water bridges: B:D.118, B:K.119 MPD.20: 2 residues within 4Å: Chain B: V.311, L.312 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.312 MPD.21: 4 residues within 4Å: Chain B: D.173, H.176, S.177, R.206 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.173, B:H.176 MPD.22: 3 residues within 4Å: Chain B: Q.165, P.191, P.193 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.165, B:P.191 Water bridges: B:Q.165

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

SO4.9: 4 residues within 4Å: Chain A: E.155, G.159, R.160, K.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.155 SO4.10: 4 residues within 4Å: Chain A: Q.63, R.70, M.93, E.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.63, A:E.100 Salt bridges: A:R.70 SO4.11: 5 residues within 4Å: Chain A: C.5, L.31, G.32, H.246, K.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.32 Salt bridges: A:K.247 SO4.23: 2 residues within 4Å: Chain B: Q.63, E.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.63 SO4.24: 4 residues within 4Å: Chain B: E.4, C.5, D.78, H.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.78 Salt bridges: B:H.246 SO4.25: 5 residues within 4Å: Chain B: E.155, L.156, G.159, R.160, K.161 No protein-ligand interaction detected (PLIP) SO4.26: 5 residues within 4Å: Chain B: C.5, L.31, G.32, F.33, H.246 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.246 SO4.27: 3 residues within 4Å: Chain B: F.43, W.52, Y.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.84, B:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandhi, A.K. et al., Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme. To be Published

Release Date

2009-11-03

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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