SMTL ID : 6p0y.1

Cryptosporidium parvum pyruvate kinase in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: T.51, I.52, P.54, R.74, N.76, H.79, G.80, R.116, S.362, G.363, A.366, N.367 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.52, A:N.76 Water bridges: A:R.74, A:R.74, A:S.362, A:S.362 Salt bridges: A:R.74, A:H.79, A:R.116 pi-Stacking: A:H.79 ADP.5: 14 residues within 4Å: Chain B: T.51, I.52, P.54, R.74, N.76, H.79, G.80, R.116, D.170, S.362, G.363, A.366, N.367 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:I.52, B:N.76 Water bridges: B:R.74, B:R.74, B:S.78, B:D.170, B:S.362, B:S.362 Salt bridges: B:R.74, B:H.79, B:R.116 pi-Stacking: B:H.79 ADP.9: 13 residues within 4Å: Chain C: T.51, I.52, P.54, R.74, N.76, H.79, G.80, R.116, S.362, G.363, A.366, N.367 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:I.52, C:N.76 Water bridges: C:R.74, C:R.74, C:S.362, C:S.362 Salt bridges: C:R.74, C:H.79, C:R.116 pi-Stacking: C:H.79 ADP.13: 14 residues within 4Å: Chain D: T.51, I.52, P.54, R.74, N.76, H.79, G.80, R.116, D.170, S.362, G.363, A.366, N.367 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:I.52, D:N.76 Water bridges: D:R.74, D:R.74, D:S.78, D:D.170, D:S.362, D:S.362 Salt bridges: D:R.74, D:H.79, D:R.116 pi-Stacking: D:H.79

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.170 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.170 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: D.170 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: D.170 Ligands: ADP.13 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: N.76, S.78, D.109, T.110, S.236, K.270 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.78, A:D.109, A:T.110 K.7: 5 residues within 4Å: Chain B: N.76, S.78, D.109, T.110, S.236 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.78, B:D.109, B:T.110, H2O.7 K.11: 6 residues within 4Å: Chain C: N.76, S.78, D.109, T.110, S.236, K.270 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.78, C:D.109, C:T.110 K.15: 5 residues within 4Å: Chain D: N.76, S.78, D.109, T.110, S.236 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.78, D:D.109, D:T.110, H2O.16

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: T.103, K.464, K.470, T.471 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: T.103, K.464, K.470, T.471 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: T.103, K.464, K.470, T.471 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: T.103, K.464, K.470, T.471 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., An overview of structure, function, and regulation of pyruvate kinases. Protein Sci. (2019)

Release Date

2019-08-21

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase

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