SMTL ID : 6eck.1

Pyruvate Kinase Isoform L-type with phosphorylated Ser113 (pS113) in complex with FBP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 16 residues within 4Å: Chain A: L.444, T.445, K.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.445, A:K.446, A:T.447, A:S.450, A:S.450, A:G.527, A:R.529, A:R.529, A:G.531, A:S.532, A:G.533, A:Y.534, A:T.535 Water bridges: A:L.444, A:K.446, A:K.446, A:T.447, A:R.449, A:W.495, A:R.502, A:R.502, A:T.535, A:T.535 Salt bridges: A:K.446, A:R.502 FBP.8: 16 residues within 4Å: Chain B: L.444, T.445, K.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:T.445, B:K.446, B:T.447, B:S.450, B:G.527, B:R.529, B:R.529, B:G.531, B:S.532, B:G.533, B:Y.534 Water bridges: B:K.446, B:K.446, B:R.468, B:R.502, B:R.502, B:R.502, B:G.527 Salt bridges: B:K.446, B:R.502 FBP.13: 16 residues within 4Å: Chain C: L.444, T.445, K.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:T.445, C:K.446, C:T.447, C:S.450, C:S.450, C:G.527, C:R.529, C:R.529, C:G.531, C:S.532, C:G.533, C:Y.534, C:T.535 Water bridges: C:L.444, C:K.446, C:K.446, C:T.447, C:R.449, C:W.495, C:R.502, C:R.502, C:T.535, C:T.535 Salt bridges: C:K.446, C:R.502 FBP.20: 16 residues within 4Å: Chain D: L.444, T.445, K.446, T.447, R.449, S.450, W.495, R.502, G.527, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:T.445, D:K.446, D:T.447, D:S.450, D:G.527, D:R.529, D:R.529, D:G.531, D:S.532, D:G.533, D:Y.534 Water bridges: D:K.446, D:K.446, D:R.468, D:R.502, D:R.502, D:R.502, D:G.527 Salt bridges: D:K.446, D:R.502

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.57, E.399, V.402, H.404, R.458, P.459, R.480 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.399, A:R.480 Water bridges: A:P.459 GOL.3: 5 residues within 4Å: Chain A: R.86, N.88, D.191, S.375, G.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.86, A:R.86, A:D.191 GOL.9: 13 residues within 4Å: Chain B: R.56, S.57, T.58, S.59, N.83, D.370, V.476, H.477, L.478, S.479, R.480, G.481, V.482 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.56, B:S.59, B:D.370, B:S.479, B:G.481, B:V.482 Water bridges: B:R.56, B:N.83, B:H.477, B:H.477 GOL.14: 7 residues within 4Å: Chain C: S.57, E.399, V.402, H.404, R.458, P.459, R.480 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.399, C:R.480 Water bridges: C:P.459 GOL.15: 5 residues within 4Å: Chain C: R.86, N.88, D.191, S.375, G.376 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.86, C:R.86, C:D.191 GOL.21: 13 residues within 4Å: Chain D: R.56, S.57, T.58, S.59, N.83, D.370, V.476, H.477, L.478, S.479, R.480, G.481, V.482 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.56, D:S.59, D:D.370, D:S.479, D:G.481, D:V.482 Water bridges: D:R.56, D:N.83, D:H.477, D:H.477

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: R.539, L.541, S.542 Chain B: W.528, N.536 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.539, A:S.542, B:N.536 Water bridges: A:V.540 PEG.11: 8 residues within 4Å: Chain B: S.57, E.399, H.404, S.455, R.458, P.459, R.480, G.481 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.399, B:R.458 Water bridges: B:P.459, B:G.481 PEG.16: 5 residues within 4Å: Chain C: R.539, L.541, S.542 Chain D: W.528, N.536 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.539, C:S.542, D:N.536 Water bridges: C:V.540 PEG.23: 8 residues within 4Å: Chain D: S.57, E.399, H.404, S.455, R.458, P.459, R.480, G.481 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.399, D:R.458 Water bridges: D:P.459, D:G.481

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: I.507, S.542, S.544 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.544 EDO.6: 5 residues within 4Å: Chain A: A.54, A.55, R.56, H.392, R.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.56, A:R.396 EDO.7: 3 residues within 4Å: Chain A: M.389, M.390 Chain C: E.317 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.317 Water bridges: A:E.386 EDO.17: 3 residues within 4Å: Chain C: I.507, S.542, S.544 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.544 EDO.18: 5 residues within 4Å: Chain C: A.54, A.55, R.56, H.392, R.396 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.56, C:R.396 EDO.19: 3 residues within 4Å: Chain A: E.317 Chain C: M.389, M.390 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.317 Water bridges: C:E.386

2 x FLC: CITRATE ANION(Non-covalent)

FLC.10: 7 residues within 4Å: Chain B: T.63, R.86, N.88, S.90, T.341, S.375, G.376 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.88, B:S.90, B:T.341, B:S.375 Water bridges: B:N.88, B:S.256 Salt bridges: B:H.91, B:K.380 FLC.22: 7 residues within 4Å: Chain D: T.63, R.86, N.88, S.90, T.341, S.375, G.376 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.88, D:S.90, D:T.341, D:S.375 Water bridges: D:N.88, D:S.256 Salt bridges: D:H.91, D:K.380

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 9 residues within 4Å: Chain B: F.39, L.366, V.402, Y.403, Q.406, L.407, E.410 Chain D: F.39, L.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.403 Water bridges: B:H.42, B:A.401 PGE.24: 9 residues within 4Å: Chain B: F.39, L.40 Chain D: F.39, L.366, V.402, Y.403, Q.406, L.407, E.410 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.403 Water bridges: D:H.42, D:A.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gassaway, B.M. et al., Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production. Cell Rep (2019)

Release Date

2019-12-04

Peptides

Pyruvate kinase PKLR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase PKLR

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