SMTL ID : 1a49.2 (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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.76, A:D.112, A:T.113, H2O.10 K.6: 7 residues within 4Å: Chain B: N.74, S.76, D.112, T.113, S.242, K.269 Ligands: ATP.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.76, B:D.112, B:T.113, H2O.13 K.11: 6 residues within 4Å: Chain C: N.74, S.76, D.112, T.113, S.242 Ligands: ATP.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.76, C:D.112, C:T.113, H2O.23 K.16: 4 residues within 4Å: Chain D: N.74, S.76, D.112, T.113 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.76, D:D.112, D:T.113, H2O.32, H2O.33

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 12 residues within 4Å: Chain A: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327, M.359 Ligands: MG.3, ATP.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.294, A:D.295, A:T.327 Water bridges: A:R.72, A:R.72, A:S.242, A:K.269 Salt bridges: A:R.72, A:K.269 OXL.7: 12 residues within 4Å: Chain B: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327, M.359 Ligands: MG.8, ATP.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.294, B:D.295, B:D.295, B:D.295, B:T.327, B:T.327 Water bridges: B:R.72 Salt bridges: B:R.72, B:K.269, B:K.269 OXL.12: 12 residues within 4Å: Chain C: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327, M.359 Ligands: MG.13, ATP.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.271, C:G.294, C:D.295, C:T.327, C:T.327 Water bridges: C:R.72, C:R.72, C:K.269 Salt bridges: C:R.72, C:K.269, C:K.269 OXL.17: 10 residues within 4Å: Chain D: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.294, D:D.295, D:T.327 Water bridges: D:R.72, D:S.242, D:D.295 Salt bridges: D:R.72, D:K.269, 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.6 MG.4: 1 residues within 4Å: Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain B: K.269, E.271, D.295 Ligands: OXL.7, ATP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.271, B:D.295, H2O.13 MG.9: 1 residues within 4Å: Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: E.271, D.295 Ligands: OXL.12, ATP.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.271, C:D.295, H2O.21 MG.14: 1 residues within 4Å: Ligands: ATP.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain D: K.269, E.271, D.295 Ligands: OXL.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.271, D:D.295, H2O.35, H2O.35

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

ATP.5: 19 residues within 4Å: Chain A: T.49, P.52, R.72, N.74, H.77, Y.82, H.83, R.119, K.206, K.269, D.295, S.361, G.362, A.365, K.366 Ligands: K.1, OXL.2, MG.3, MG.4 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:N.74, A:K.206, A:K.206, A:S.361 Water bridges: A:I.50, A:I.50, A:R.72, A:R.72, A:N.74, A:H.77, A:H.77, A:H.83, A:R.119, A:D.176, A:D.176, A:D.176, A:D.177, A:K.206, A:S.242, A:S.242, A:G.362 Salt bridges: A:R.72, A:R.72, A:H.77, A:R.119, A:R.119, A:K.269 pi-Stacking: A:H.77 ATP.10: 21 residues within 4Å: Chain B: T.49, I.50, P.52, R.72, N.74, H.77, Y.82, H.83, D.112, R.119, K.206, K.269, D.295, S.361, G.362, A.365, K.366 Ligands: K.6, OXL.7, MG.8, MG.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:I.50, B:N.74, B:Y.82, B:K.206 Water bridges: B:R.72, B:R.72, B:E.117, B:E.117, B:R.119, B:D.177, B:S.242, B:K.269, B:D.295, B:S.361 Salt bridges: B:R.72, B:R.72, B:H.77, B:R.119, B:K.269 pi-Stacking: B:H.77 ATP.15: 17 residues within 4Å: Chain C: T.49, P.52, R.72, N.74, H.77, Y.82, H.83, R.119, K.206, D.295, S.361, G.362, A.365 Ligands: K.11, OXL.12, MG.13, MG.14 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:N.74, C:N.74, C:K.206, C:K.206 Water bridges: C:I.50, C:R.72, C:R.72, C:N.74, C:G.78, C:H.83, C:R.119, C:R.119, C:D.176, C:D.176, C:D.176, C:D.177, C:S.242, C:K.269, C:S.361, C:G.362 Salt bridges: C:R.72, C:R.72, C:H.77, C:R.119, C:R.119, C:K.269 pi-Stacking: C: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
E

B
F

C
G

D
H

PYRUVATE KINASE

Related Entries With Identical Sequence