SMTL ID : 3srd.1

Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and Oxalate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 7 residues within 4Å: Chain A: K.290, E.292, A.313, G.315, D.316, T.348 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.315, A:D.316, A:T.348 Water bridges: A:K.290 Salt bridges: A:R.93, A:K.290, A:K.290 OXL.6: 8 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:T.348, B:T.348 Salt bridges: B:R.93, B:K.290, B:K.290 OXL.11: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.315, C:D.316, C:T.348 Salt bridges: C:R.93, C:K.290 OXL.16: 10 residues within 4Å: Chain D: K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.315, D:D.316, D:T.348, D:T.348 Salt bridges: D:R.93, D:K.290, D:K.290

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

FBP.2: 17 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, W.535, R.536, P.537, G.538, S.539, G.540, F.541, T.542 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:R.456, A:S.457, A:S.457, A:S.457, A:G.534, A:R.536, A:R.536, A:G.538, A:S.539, A:G.540, A:F.541 Salt bridges: A:K.453, A:R.509 FBP.8: 16 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, S.457, W.502, R.509, T.533, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.452, B:K.453, B:S.454, B:S.457, B:S.457, B:S.457, B:G.534, B:R.536, B:G.538, B:G.540, B:F.541 Salt bridges: B:K.453, B:R.509 FBP.10: 16 residues within 4Å: Chain C: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.452, C:T.452, C:K.453, C:S.454, C:G.455, C:R.456, C:S.457, C:S.457, C:S.457, C:G.534, C:R.536, C:G.538, C:G.540, C:F.541 Salt bridges: C:K.453, C:R.509 FBP.15: 16 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.452, D:K.453, D:S.454, D:R.456, D:S.457, D:S.457, D:S.457, D:G.534, D:G.534, D:G.538, D:G.540, D:F.541 Salt bridges: D:K.453, D:R.509

3 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263, K.290 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.133, A:T.134 K.13: 6 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263, K.290 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.133, C:T.134 K.18: 5 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, S.263 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.133, D:T.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.1 MG.7: 3 residues within 4Å: Chain B: E.292, D.316 Ligands: OXL.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.12: 3 residues within 4Å: Chain C: E.292, D.316 Ligands: OXL.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.17: 3 residues within 4Å: Chain D: E.292, D.316 Ligands: OXL.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: R.63, N.64, G.66, N.90, H.484, Y.486, I.489, F.490, P.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.90, A:N.90, A:H.484, A:I.489 GOL.9: 8 residues within 4Å: Chain B: R.63, N.64, G.66, N.90, H.484, I.489, F.490, P.491 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.90, B:H.484, B:H.484, B:I.489 GOL.14: 8 residues within 4Å: Chain C: R.63, N.64, G.66, N.90, H.484, Y.486, I.489, F.490 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.64, C:I.489 Water bridges: C:R.63, C:R.63 GOL.19: 8 residues within 4Å: Chain D: R.63, N.64, G.66, N.90, H.484, I.489, F.490, P.491 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.90, D:N.90, D:H.484, D:H.484 GOL.20: 7 residues within 4Å: Chain D: P.137, V.229, N.230, L.231, V.236, F.264, E.320 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.229, D:N.230, D:L.231, D:E.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., Allosetric regulation of M2 pyruvate kinase. To be Published

Release Date

2012-08-08

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes M1/M2

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