SMTL ID : 1a49.1 (1 other biounit)

BIS MG-ATP-K-OXALATE COMPLEX OF PYRUVATE KINASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: N.74, S.76, D.112, T.113, S.242 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.76, A:D.112, A:T.113 K.6: 6 residues within 4Å: Chain B: N.74, S.76, D.112, T.113, S.242, K.269 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.112, B:T.113, H2O.10 K.9: 6 residues within 4Å: Chain C: N.74, S.76, D.112, T.113, S.242 Ligands: ATP.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.76, C:D.112, C:T.113 K.14: 7 residues within 4Å: Chain D: N.74, S.76, D.112, T.113, S.242, K.269 Ligands: ATP.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.76, D:D.112, D:T.113, H2O.33

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 11 residues within 4Å: Chain A: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MG.3, ATP.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.271, A:G.294, A:D.295, A:D.295, A:T.327, A:T.327 Water bridges: A:K.269 Salt bridges: A:R.72, A:K.269, A:K.269 OXL.7: 9 residues within 4Å: Chain B: K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.271, B:G.294, B:D.295, B:T.327 Water bridges: B:R.72, B:K.269 Salt bridges: B:R.72, B:K.269, B:K.269 OXL.10: 11 residues within 4Å: Chain C: R.72, K.269, E.271, A.292, R.293, G.294, D.295, T.327, M.359 Ligands: MG.11, ATP.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.294, C:D.295, C:T.327 Water bridges: C:R.72, C:R.72 Salt bridges: C:R.72, C:K.269, C:K.269 OXL.15: 12 residues within 4Å: Chain D: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327, M.359 Ligands: MG.16, ATP.18 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.271, D:G.294, D:D.295, D:D.295, D:D.295, D:T.327, D:T.327 Water bridges: D:R.72, D:S.361 Salt bridges: D:R.72, D:K.269

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: E.271, D.295 Ligands: OXL.2, ATP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.271, A:D.295, H2O.4 MG.4: 1 residues within 4Å: Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: E.271, D.295 Ligands: OXL.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.271, B:D.295, H2O.15 MG.11: 5 residues within 4Å: Chain C: K.269, E.271, D.295 Ligands: OXL.10, ATP.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.271, C:D.295 MG.12: 1 residues within 4Å: Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain D: K.269, E.271, D.295 Ligands: OXL.15, ATP.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.271, D:D.295, H2O.28 MG.17: 1 residues within 4Å: Ligands: ATP.18 No protein-ligand interaction detected (PLIP)

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

ATP.5: 20 residues within 4Å: Chain A: T.49, P.52, R.72, N.74, H.77, Y.82, H.83, R.119, G.127, K.206, K.269, D.295, S.361, G.362, A.365, K.366 Ligands: K.1, OXL.2, MG.3, MG.4 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:I.50, A:N.74, A:K.206, A:K.206, A:D.295 Water bridges: A:H.83, A:R.119, A:R.119, A:R.119, A:D.176, A:D.176, A:D.177, A:K.269, A:K.269, A:T.327 Salt bridges: A:R.72, A:R.72, A:H.77, A:H.77, A:R.119, A:R.119, A:K.269 pi-Stacking: A:H.77, A:H.77 ATP.13: 19 residues within 4Å: Chain C: T.49, P.52, R.72, N.74, H.77, Y.82, H.83, R.119, D.177, K.206, D.295, S.361, G.362, A.365, K.366 Ligands: K.9, OXL.10, MG.11, MG.12 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.74, C:D.177, C:K.206 Water bridges: C:R.72, C:H.83, C:R.119, C:R.119, C:D.176, C:G.362 Salt bridges: C:R.72, C:R.72, C:H.77, C:H.77, C:R.119, C:R.119, C:K.269 pi-Stacking: C:H.77 ATP.18: 21 residues within 4Å: Chain D: T.49, P.52, R.72, N.74, H.77, Y.82, H.83, R.119, G.127, D.177, K.206, K.269, D.295, S.361, G.362, A.365, K.366 Ligands: K.14, OXL.15, MG.16, MG.17 29 PLIP interactions: 29 interactions with chain D Hydrogen bonds: D:I.50, D:N.74, D:D.177, D:K.206, D:K.206 Water bridges: D:R.72, D:H.77, D:H.77, D:H.83, D:R.119, D:R.119, D:R.119, D:D.176, D:D.176, D:D.176, D:D.177, D:S.242, D:K.269, D:K.269, D:S.361, D:K.366, D:K.366 Salt bridges: D:R.72, D:R.72, D:H.77, D:R.119, D:R.119, D:K.269 pi-Stacking: D:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsen, T.M. et al., Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel. Biochemistry (1998)

Release Date

1999-04-20

Peptides

PYRUVATE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PYRUVATE KINASE

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