SMTL ID : 7z4n.1

Plasmodium falciparum pyruvate kinase complexed with pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.257, D.281 Ligands: PYR.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.257, A:D.281, H2O.2, H2O.3, PYR.3 MG.18: 3 residues within 4Å: Chain B: E.257, D.281 Ligands: PYR.20 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.257, B:D.281, H2O.8, H2O.10, PYR.20 MG.35: 3 residues within 4Å: Chain C: E.257, D.281 Ligands: PYR.37 5 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:E.257, C:D.281, H2O.14, H2O.16, PYR.37 MG.52: 3 residues within 4Å: Chain D: E.257, D.281 Ligands: PYR.54 5 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:E.257, D:D.281, H2O.20, H2O.22, PYR.54

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: N.69, S.71, D.102, T.103, S.228, K.255 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.71, A:D.102, A:T.103 K.19: 6 residues within 4Å: Chain B: N.69, S.71, D.102, T.103, S.228, K.255 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.71, B:D.102, B:T.103 K.36: 6 residues within 4Å: Chain C: N.69, S.71, D.102, T.103, S.228, K.255 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.71, C:D.102, C:T.103 K.53: 6 residues within 4Å: Chain D: N.69, S.71, D.102, T.103, S.228, K.255 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.71, D:D.102, D:T.103

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 11 residues within 4Å: Chain A: R.67, K.255, E.257, A.278, R.279, G.280, D.281, T.313, M.345 Ligands: MG.1, PEG.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.255, A:G.280, A:D.281, A:T.313, A:T.313 Water bridges: A:R.67 PYR.20: 11 residues within 4Å: Chain B: R.67, K.255, E.257, A.278, R.279, G.280, D.281, T.313, M.345 Ligands: MG.18, PEG.24 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.255, B:G.280, B:D.281, B:T.313, B:T.313 Water bridges: B:R.67 PYR.37: 11 residues within 4Å: Chain C: R.67, K.255, E.257, A.278, R.279, G.280, D.281, T.313, M.345 Ligands: MG.35, PEG.41 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.255, C:G.280, C:D.281, C:T.313 Water bridges: C:R.67 PYR.54: 11 residues within 4Å: Chain D: R.67, K.255, E.257, A.278, R.279, G.280, D.281, T.313, M.345 Ligands: MG.52, PEG.58 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.255, D:G.280, D:D.281, D:T.313 Water bridges: D:R.67

28 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: G.221, N.223, S.443, K.446 Ligands: PEG.5 Ligand excluded by PLIP PEG.5: 8 residues within 4Å: Chain A: F.82, L.86, Q.89, L.97, M.99, M.220, K.446 Ligands: PEG.4 Ligand excluded by PLIP PEG.7: 7 residues within 4Å: Chain A: D.162, N.192, G.280, D.281, T.313 Ligands: PYR.3, GOL.15 Ligand excluded by PLIP PEG.8: 7 residues within 4Å: Chain A: Q.25, E.28, N.30, L.368, E.369, A.372 Chain B: K.290 Ligand excluded by PLIP PEG.9: 5 residues within 4Å: Chain A: D.234, R.237, L.238, N.241 Ligands: GOL.13 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: A.233, D.234, R.237, K.267 Ligand excluded by PLIP PEG.11: 11 residues within 4Å: Chain A: M.15, S.17, N.303, V.337, L.338, D.339, G.340, I.374, L.379, K.430, R.452 Ligand excluded by PLIP PEG.21: 5 residues within 4Å: Chain B: G.221, N.223, S.443, K.446 Ligands: PEG.22 Ligand excluded by PLIP PEG.22: 8 residues within 4Å: Chain B: F.82, L.86, Q.89, L.97, M.99, M.220, K.446 Ligands: PEG.21 Ligand excluded by PLIP PEG.24: 7 residues within 4Å: Chain B: D.162, N.192, G.280, D.281, T.313 Ligands: PYR.20, GOL.32 Ligand excluded by PLIP PEG.25: 7 residues within 4Å: Chain A: K.290 Chain B: Q.25, E.28, N.30, L.368, E.369, A.372 Ligand excluded by PLIP PEG.26: 5 residues within 4Å: Chain B: D.234, R.237, L.238, N.241 Ligands: GOL.30 Ligand excluded by PLIP PEG.27: 4 residues within 4Å: Chain B: A.233, D.234, R.237, K.267 Ligand excluded by PLIP PEG.28: 11 residues within 4Å: Chain B: M.15, S.17, N.303, V.337, L.338, D.339, G.340, I.374, L.379, K.430, R.452 Ligand excluded by PLIP PEG.38: 5 residues within 4Å: Chain C: G.221, N.223, S.443, K.446 Ligands: PEG.39 Ligand excluded by PLIP PEG.39: 8 residues within 4Å: Chain C: F.82, L.86, Q.89, L.97, M.99, M.220, K.446 Ligands: PEG.38 Ligand excluded by PLIP PEG.41: 7 residues within 4Å: Chain C: D.162, N.192, G.280, D.281, T.313 Ligands: PYR.37, GOL.49 Ligand excluded by PLIP PEG.42: 7 residues within 4Å: Chain C: Q.25, E.28, N.30, L.368, E.369, A.372 Chain D: K.290 Ligand excluded by PLIP PEG.43: 5 residues within 4Å: Chain C: D.234, R.237, L.238, N.241 Ligands: GOL.47 Ligand excluded by PLIP PEG.44: 4 residues within 4Å: Chain C: A.233, D.234, R.237, K.267 Ligand excluded by PLIP PEG.45: 11 residues within 4Å: Chain C: M.15, S.17, N.303, V.337, L.338, D.339, G.340, I.374, L.379, K.430, R.452 Ligand excluded by PLIP PEG.55: 5 residues within 4Å: Chain D: G.221, N.223, S.443, K.446 Ligands: PEG.56 Ligand excluded by PLIP PEG.56: 8 residues within 4Å: Chain D: F.82, L.86, Q.89, L.97, M.99, M.220, K.446 Ligands: PEG.55 Ligand excluded by PLIP PEG.58: 7 residues within 4Å: Chain D: D.162, N.192, G.280, D.281, T.313 Ligands: PYR.54, GOL.66 Ligand excluded by PLIP PEG.59: 7 residues within 4Å: Chain C: K.290 Chain D: Q.25, E.28, N.30, L.368, E.369, A.372 Ligand excluded by PLIP PEG.60: 5 residues within 4Å: Chain D: D.234, R.237, L.238, N.241 Ligands: GOL.64 Ligand excluded by PLIP PEG.61: 4 residues within 4Å: Chain D: A.233, D.234, R.237, K.267 Ligand excluded by PLIP PEG.62: 11 residues within 4Å: Chain D: M.15, S.17, N.303, V.337, L.338, D.339, G.340, I.374, L.379, K.430, R.452 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: P.106, M.193, N.194, L.195, V.200, F.229, E.285 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: R.240, R.248, H.249, I.250, K.251, D.273 Ligands: GOL.16 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: I.205, D.234, D.235, L.238 Ligands: PEG.9 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: R.35, K.37, H.40, G.62, D.64, T.455 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: H.72, R.109, A.161, D.162, K.191, N.192 Ligands: PEG.7 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: V.236, R.240, I.252, E.271, D.273 Ligands: GOL.12 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: P.106, M.193, N.194, L.195, V.200, F.229, E.285 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain B: R.240, R.248, H.249, I.250, K.251, D.273 Ligands: GOL.33 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: I.205, D.234, D.235, L.238 Ligands: PEG.26 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain B: R.35, K.37, H.40, G.62, D.64, T.455 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain B: H.72, R.109, A.161, D.162, K.191, N.192 Ligands: PEG.24 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain B: V.236, R.240, I.252, E.271, D.273 Ligands: GOL.29 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain C: P.106, M.193, N.194, L.195, V.200, F.229, E.285 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain C: R.240, R.248, H.249, I.250, K.251, D.273 Ligands: GOL.50 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain C: I.205, D.234, D.235, L.238 Ligands: PEG.43 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain C: R.35, K.37, H.40, G.62, D.64, T.455 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain C: H.72, R.109, A.161, D.162, K.191, N.192 Ligands: PEG.41 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain C: V.236, R.240, I.252, E.271, D.273 Ligands: GOL.46 Ligand excluded by PLIP GOL.57: 7 residues within 4Å: Chain D: P.106, M.193, N.194, L.195, V.200, F.229, E.285 Ligand excluded by PLIP GOL.63: 7 residues within 4Å: Chain D: R.240, R.248, H.249, I.250, K.251, D.273 Ligands: GOL.67 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain D: I.205, D.234, D.235, L.238 Ligands: PEG.60 Ligand excluded by PLIP GOL.65: 6 residues within 4Å: Chain D: R.35, K.37, H.40, G.62, D.64, T.455 Ligand excluded by PLIP GOL.66: 7 residues within 4Å: Chain D: H.72, R.109, A.161, D.162, K.191, N.192 Ligands: PEG.58 Ligand excluded by PLIP GOL.67: 6 residues within 4Å: Chain D: V.236, R.240, I.252, E.271, D.273 Ligands: GOL.63 Ligand excluded by PLIP

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.17: 8 residues within 4Å: Chain A: N.33, R.35, D.60, L.91, R.92, P.93, N.94, C.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.33, A:N.94, A:N.94, A:C.95 MES.34: 8 residues within 4Å: Chain B: N.33, R.35, D.60, L.91, R.92, P.93, N.94, C.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.33, B:N.94, B:N.94, B:C.95 MES.51: 8 residues within 4Å: Chain C: N.33, R.35, D.60, L.91, R.92, P.93, N.94, C.95 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.33, C:N.94, C:N.94, C:C.95 MES.68: 8 residues within 4Å: Chain D: N.33, R.35, D.60, L.91, R.92, P.93, N.94, C.95 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.33, D:N.94, D:N.94, D:C.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dillenberger, M. et al., Prominent role of cysteine residues C49 and C343 in regulating Plasmodium falciparum pyruvate kinase activity. Structure (2022)

Release Date

2022-08-24

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyruvate kinase

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