- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 7 x SIN: SUCCINIC ACID(Non-covalent)
SIN.2: 12 residues within 4Å:- Chain A: R.73, K.270, E.272, A.293, G.295, D.296, T.328, M.360, S.362
- Ligands: ADP.1, MN.3, MN.5
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:A.293
- Hydrogen bonds: A:G.295, A:D.296, A:S.362
- Water bridges: A:R.73, A:N.75
- Salt bridges: A:R.73, A:K.270, A:K.270
SIN.6: 7 residues within 4Å:- Chain A: T.432, E.433, S.434, R.436, S.437, G.520, F.521
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.433, A:S.434, A:S.434, A:S.437
- Salt bridges: A:R.436
SIN.12: 12 residues within 4Å:- Chain B: R.73, K.270, E.272, A.293, G.295, D.296, T.328, M.360, S.362
- Ligands: ADP.11, MN.13, MN.14
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:A.293
- Hydrogen bonds: B:G.295, B:D.296, B:S.362
- Water bridges: B:R.73, B:K.270, B:K.270
- Salt bridges: B:R.73, B:K.270
SIN.16: 7 residues within 4Å:- Chain B: T.432, E.433, S.434, R.436, S.437, G.520, F.521
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:T.432, B:E.433, B:S.434, B:S.434, B:S.434, B:R.436, B:S.437
- Salt bridges: B:R.436
SIN.24: 12 residues within 4Å:- Chain C: R.73, K.270, E.272, A.293, G.295, D.296, T.328, M.360, S.362
- Ligands: ADP.23, MN.25, MN.26
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:A.293
- Hydrogen bonds: C:G.295, C:D.296, C:S.362
- Water bridges: C:R.73, C:N.75, C:D.178
- Salt bridges: C:R.73, C:K.270
SIN.28: 7 residues within 4Å:- Chain C: T.432, E.433, S.434, R.436, S.437, G.520, F.521
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:T.432, C:E.433, C:S.434, C:S.434, C:S.437, C:S.437
SIN.35: 7 residues within 4Å:- Chain D: T.432, E.433, S.434, R.436, S.437, G.520, F.521
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:T.432, D:E.433, D:S.434, D:S.434, D:R.436, D:R.436, D:S.437, D:S.437, D:G.520
- 8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)
MN.3: 3 residues within 4Å:- Chain A: E.272, D.296
- Ligands: SIN.2
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.272, A:D.296, H2O.2, H2O.7
MN.5: 2 residues within 4Å:- Ligands: ADP.1, SIN.2
No protein-ligand interaction detected (PLIP)MN.13: 3 residues within 4Å:- Chain B: D.178
- Ligands: ADP.11, SIN.12
No protein-ligand interaction detected (PLIP)MN.14: 4 residues within 4Å:- Chain B: K.270, E.272, D.296
- Ligands: SIN.12
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.272, B:D.296, H2O.19, H2O.21
MN.25: 3 residues within 4Å:- Chain C: D.178
- Ligands: ADP.23, SIN.24
No protein-ligand interaction detected (PLIP)MN.26: 3 residues within 4Å:- Chain C: E.272, D.296
- Ligands: SIN.24
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.272, C:D.296, H2O.26, H2O.27
MN.32: 3 residues within 4Å:- Chain D: E.272, D.296
- Ligands: GZ3.31
5 PLIP interactions:2 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:E.272, D:D.296, H2O.42, H2O.49, H2O.50
MN.33: 2 residues within 4Å:- Chain D: D.296
- Ligands: GZ3.31
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.296, H2O.52, H2O.52
- 4 x K: POTASSIUM ION(Non-covalent)
K.4: 6 residues within 4Å:- Chain A: N.75, S.77, D.113, T.114, S.243, K.270
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:S.77, A:D.113, A:T.114, H2O.4
K.15: 5 residues within 4Å:- Chain B: N.75, S.77, D.113, T.114, S.243
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:S.77, B:D.113, B:T.114, H2O.18
K.27: 5 residues within 4Å:- Chain C: N.75, S.77, D.113, T.114, S.243
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:S.77, C:D.113, C:T.114, H2O.30
K.34: 6 residues within 4Å:- Chain D: N.75, S.77, D.113, T.114, K.270
- Ligands: GZ3.31
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:S.77, D:D.113, D:T.114, H2O.50
- 4 x ALA: ALANINE(Non-covalent)
ALA.7: 8 residues within 4Å:- Chain A: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471
8 PLIP interactions:7 interactions with chain A, 1 Ligand-Ligand interactions- Hydrogen bonds: A:N.70, A:H.464, A:I.469, A.7
- Water bridges: A:R.106
- Salt bridges: A:R.43, A:R.106, A:H.464
ALA.17: 8 residues within 4Å:- Chain B: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471
8 PLIP interactions:7 interactions with chain B, 1 Ligand-Ligand interactions- Hydrogen bonds: B:N.70, B:H.464, B:I.469, A.17
- Water bridges: B:R.106
- Salt bridges: B:R.43, B:R.106, B:H.464
ALA.29: 8 residues within 4Å:- Chain C: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:N.70, C:N.70, C:H.464
- Water bridges: C:N.44, C:R.106, C:H.464
- Salt bridges: C:R.106, C:H.464
ALA.36: 8 residues within 4Å:- Chain D: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:N.70, D:N.70, D:H.464
- Water bridges: D:N.44, D:R.106
- Salt bridges: D:R.43, D:R.106, D:H.464
- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 9 residues within 4Å:- Chain A: D.178, G.179, L.180, Q.329
- Chain D: K.337, R.339, P.340, T.341, R.342
7 PLIP interactions:6 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:R.339, D:R.342, D:R.342, A:Q.329
- Water bridges: D:K.337, D:K.337, D:R.339
GOL.9: 5 residues within 4Å:- Chain A: V.277, R.278, M.312, R.316
- Chain D: D.34
6 PLIP interactions:2 interactions with chain D, 4 interactions with chain A- Hydrogen bonds: D:D.34, D:I.35, A:R.316, A:R.316
- Water bridges: A:F.280, A:D.281
GOL.10: 9 residues within 4Å:- Chain A: M.22, R.392, E.418, Y.421, K.422
- Chain C: A.399, R.400, S.403, M.414
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:R.392
- Water bridges: C:R.400
GOL.18: 5 residues within 4Å:- Chain B: R.392, Y.421, K.422
- Chain D: A.399, S.403
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:A.399
- Water bridges: D:S.403, B:Y.421
GOL.19: 5 residues within 4Å:- Chain B: D.407, E.410, R.436, Q.440, R.443
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:D.407, B:E.410, B:R.436, B:R.436, B:R.443
- Water bridges: B:A.320, B:S.405, B:Q.440
GOL.20: 6 residues within 4Å:- Chain B: A.399, R.400, S.403
- Chain D: R.392, K.422
- Ligands: GOL.37
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.399
- Water bridges: B:S.403, B:S.405
GOL.21: 7 residues within 4Å:- Chain B: F.26, L.353, D.354, L.394
- Chain C: F.26, L.27, M.30
2 PLIP interactions:2 interactions with chain C- Water bridges: C:L.27, C:L.27
GOL.22: 10 residues within 4Å:- Chain B: D.177, D.178, G.179, L.180, Q.329
- Chain C: K.337, R.339, P.340, T.341, R.342
7 PLIP interactions:3 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: B:Q.329, B:Q.329, C:R.342
- Water bridges: B:G.179, C:R.339, C:R.342, C:R.342
GOL.30: 9 residues within 4Å:- Chain B: K.337, R.339, P.340, T.341, R.342
- Chain C: D.178, G.179, L.180, Q.329
8 PLIP interactions:3 interactions with chain C, 5 interactions with chain B- Hydrogen bonds: C:D.178, C:G.179, C:Q.329, B:R.342, B:R.342
- Water bridges: B:K.337, B:K.337, B:R.339
GOL.37: 8 residues within 4Å:- Chain B: F.395, E.396
- Chain D: R.392, F.395, E.396, E.418, Y.421
- Ligands: GOL.20
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.396, D:E.396
GOL.38: 5 residues within 4Å:- Chain D: D.407, E.410, R.436, Q.440, R.443
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:D.407, D:R.436, D:R.436, D:R.443, D:R.443
- Water bridges: D:A.320, D:S.405, D:Q.440
GOL.39: 8 residues within 4Å:- Chain D: P.117, I.119, V.209, N.210, L.211, V.216, F.244, E.300
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:P.117, D:N.210, D:L.211
- Water bridges: D:I.119, D:L.211, D:E.300
GOL.40: 7 residues within 4Å:- Chain D: A.215, V.216, D.217, R.246, K.247, E.275, R.279
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:V.216, D:R.246, D:E.275, D:R.279
- 1 x GZ3: (E)-2-METHYL-3-PHOSPHONOACRYLATE(Non-covalent)
GZ3.31: 12 residues within 4Å:- Chain D: R.73, K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328
- Ligands: MN.32, MN.33, K.34
9 PLIP interactions:9 interactions with chain D- Hydrophobic interactions: D:A.293
- Hydrogen bonds: D:R.73, D:K.270, D:G.295, D:D.296, D:T.328, D:T.328
- Water bridges: D:S.77, D:S.77
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Swint-Kruse, L. et al., PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) (2023)
- Release Date
- 2023-05-24
- Peptides
- Pyruvate kinase PKM: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
CC
DD
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 7 x SIN: SUCCINIC ACID(Non-covalent)
- 8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x ALA: ALANINE(Non-covalent)
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 1 x GZ3: (E)-2-METHYL-3-PHOSPHONOACRYLATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Swint-Kruse, L. et al., PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) (2023)
- Release Date
- 2023-05-24
- Peptides
- Pyruvate kinase PKM: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
CC
DD
E