SMTL ID : 2vgi.1

HUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 17 residues within 4Å: Chain A: L.428, T.429, T.430, T.431, G.432, R.433, S.434, W.479, R.486, G.511, R.513, P.514, G.515, S.516, G.517, Y.518, T.519 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.429, A:T.429, A:T.430, A:T.430, A:T.431, A:G.432, A:S.434, A:S.434, A:G.511, A:G.515, A:S.516, A:G.517, A:Y.518, A:T.519 Salt bridges: A:R.486 FBP.5: 17 residues within 4Å: Chain B: L.428, T.429, T.430, T.431, G.432, R.433, S.434, W.479, R.486, G.511, R.513, P.514, G.515, S.516, G.517, Y.518, T.519 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.429, B:T.430, B:T.430, B:T.431, B:G.432, B:R.433, B:S.434, B:S.434, B:G.511, B:R.513, B:G.515, B:S.516, B:G.517, B:Y.518 Salt bridges: B:R.486 FBP.9: 17 residues within 4Å: Chain C: L.428, T.429, T.430, T.431, G.432, R.433, S.434, W.479, R.486, G.511, R.513, P.514, G.515, S.516, G.517, Y.518, T.519 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.429, C:T.429, C:T.430, C:T.430, C:T.431, C:G.432, C:S.434, C:S.434, C:G.511, C:R.513, C:G.515, C:S.516, C:G.517, C:Y.518 Salt bridges: C:R.486 FBP.13: 18 residues within 4Å: Chain D: L.428, T.429, T.430, T.431, G.432, S.434, R.452, W.479, R.486, T.510, G.511, R.513, P.514, G.515, S.516, G.517, Y.518, T.519 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.429, D:T.430, D:T.430, D:T.431, D:G.432, D:S.434, D:S.434, D:R.452, D:G.511, D:R.513, D:G.515, D:S.516, D:G.517, D:Y.518, D:T.519 Salt bridges: D:R.486

4 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.2: 10 residues within 4Å: Chain A: R.70, D.110, K.267, E.269, A.290, G.292, D.293, T.325 Ligands: K.3, MN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.292, A:D.293, A:T.325 Salt bridges: A:R.70, A:K.267 PGA.6: 11 residues within 4Å: Chain B: R.70, D.110, K.267, E.269, A.290, R.291, G.292, D.293, T.325 Ligands: K.7, MN.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.292, B:D.293, B:T.325, B:T.325 Salt bridges: B:R.70, B:K.267 PGA.10: 10 residues within 4Å: Chain C: R.70, D.110, K.267, E.269, A.290, G.292, D.293, T.325 Ligands: K.11, MN.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.292, C:D.293, C:T.325 Salt bridges: C:R.70, C:K.267 PGA.14: 11 residues within 4Å: Chain D: R.70, D.110, K.267, E.269, A.290, R.291, G.292, D.293, T.325 Ligands: K.15, MN.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.72, D:E.269, D:G.292, D:D.293, D:D.293, D:D.293, D:T.325 Salt bridges: D:R.70, D:K.267

4 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: N.72, S.74, D.110, T.111, K.112, S.240, K.267 Ligands: PGA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.110, A:T.111 K.7: 7 residues within 4Å: Chain B: N.72, S.74, D.110, T.111, S.240, K.267 Ligands: PGA.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.110 K.11: 5 residues within 4Å: Chain C: N.72, S.74, D.110, T.111 Ligands: PGA.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:S.74, C:D.110, PGA.10 K.15: 8 residues within 4Å: Chain D: N.72, S.74, D.110, T.111, K.112, S.240, K.267 Ligands: PGA.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.74, D:D.110, D:T.111

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 3 residues within 4Å: Chain A: E.269, D.293 Ligands: PGA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.269, A:D.293, PGA.2 MN.8: 3 residues within 4Å: Chain B: E.269, D.293 Ligands: PGA.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.269, B:D.293, PGA.6 MN.12: 3 residues within 4Å: Chain C: E.269, D.293 Ligands: PGA.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.269, C:D.293, PGA.10 MN.16: 3 residues within 4Å: Chain D: E.269, D.293 Ligands: PGA.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.269, D:D.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valentini, G. et al., Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia. J.Biol.Chem. (2002)

Release Date

2007-11-20

Peptides

PYRUVATE KINASE ISOZYMES R/L: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PYRUVATE KINASE ISOZYMES R/L