SMTL ID : 2phk.1

THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE COMPLEX: KINASE SUBSTRATE RECOGNITION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ARG- GLN- MET- SER- PHE- ARG- LEU: MC-PEPTIDE(Non-covalent)

ARG-GLN-MET-SER-PHE-ARG-LEU.1: 30 residues within 4Å: Chain A: V.16, E.97, F.99, R.135, D.136, K.138, E.140, F.157, E.169, V.170, C.171, G.172, T.173, P.174, S.175, L.177 Chain B: R.14, G.15, V.16, R.219, K.220, Q.221, M.222, L.223, M.224, L.225 Ligands: ATP.4, ARG-GLN-MET-SER-PHE-ARG-LEU.6, ARG-GLN-MET-SER-PHE-ARG-LEU.6, ARG-GLN-MET-SER-PHE-ARG-LEU.6 29 PLIP interactions: 10 interactions with chain B, 19 interactions with chain A Hydrophobic interactions: B:R.219, B:K.220, B:Q.221, B:Q.221, B:M.222, B:L.225, A:F.99, A:F.157, A:T.173, A:P.174, A:L.177 Hydrogen bonds: B:G.15, B:R.219, B:L.223, B:M.224, A:K.138, A:E.140, A:E.140, A:V.170, A:G.172, A:G.172, A:S.175, A:S.175 Water bridges: A:E.140, A:D.154, A:E.169, A:E.169 Salt bridges: A:E.97, A:E.169 ARG-GLN-MET-SER-PHE-ARG-LEU.6: 30 residues within 4Å: Chain A: R.14, G.15, V.16, R.219, K.220, Q.221, M.222, L.223, M.224, L.225 Chain B: V.16, E.97, F.99, R.135, D.136, K.138, E.140, F.157, E.169, V.170, C.171, G.172, T.173, P.174, S.175, L.177 Ligands: ARG-GLN-MET-SER-PHE-ARG-LEU.1, ARG-GLN-MET-SER-PHE-ARG-LEU.1, ARG-GLN-MET-SER-PHE-ARG-LEU.1, ATP.9 28 PLIP interactions: 16 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:F.99, B:F.157, B:T.173, B:P.174, B:L.177, A:R.219, A:K.220, A:Q.221, A:Q.221, A:M.222, A:L.225 Hydrogen bonds: B:K.138, B:E.140, B:G.172, B:G.172, B:S.175, B:S.175, A:R.14, A:R.219, A:L.223, A:M.224 Water bridges: B:E.140, B:D.154, B:E.169, A:M.222, A:M.222 Salt bridges: B:E.97, B:E.169

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: D.136, D.154 Ligands: MN.3, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.154, A:D.154, H2O.1, H2O.2 MN.3: 4 residues within 4Å: Chain A: N.141, D.154 Ligands: MN.2, ATP.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.154, H2O.3 MN.7: 4 residues within 4Å: Chain B: D.136, D.154 Ligands: MN.8, ATP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.154, B:D.154, H2O.5, H2O.5 MN.8: 4 residues within 4Å: Chain B: N.141, D.154 Ligands: MN.7, ATP.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.154, H2O.6

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

ATP.4: 24 residues within 4Å: Chain A: L.12, G.13, G.15, V.16, S.18, V.20, A.33, K.35, I.74, F.90, D.91, M.93, E.97, D.136, K.138, E.140, N.141, L.143, D.154 Ligands: ARG-GLN-MET-SER-PHE-ARG-LEU.1, ARG-GLN-MET-SER-PHE-ARG-LEU.1, ARG-GLN-MET-SER-PHE-ARG-LEU.1, MN.2, MN.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:V.16, A:S.18, A:D.91, A:M.93, A:E.97, A:E.97 Water bridges: A:S.18, A:K.35, A:E.140, A:N.141 Salt bridges: A:K.35, A:K.35, A:K.138 ATP.9: 24 residues within 4Å: Chain B: L.12, G.13, G.15, V.16, S.18, V.20, A.33, K.35, I.74, F.90, D.91, M.93, E.97, D.136, K.138, E.140, N.141, L.143, D.154 Ligands: ARG-GLN-MET-SER-PHE-ARG-LEU.6, ARG-GLN-MET-SER-PHE-ARG-LEU.6, ARG-GLN-MET-SER-PHE-ARG-LEU.6, MN.7, MN.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:V.16, B:S.18, B:D.91, B:M.93, B:E.97 Water bridges: B:S.18, B:K.35, B:E.140, B:N.141, B:T.153 Salt bridges: B:K.35, B:K.35, B:K.138

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.260, K.261, R.262, E.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.261 GOL.10: 4 residues within 4Å: Chain B: Q.260, K.261, R.262, E.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lowe, E.D. et al., The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition. EMBO J. (1997)

Release Date

1999-01-13

Peptides

PHOSPHORYLASE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PHOSPHORYLASE KINASE