SMTL ID : 6ech.1

Pyruvate Kinase Isoform L-type with phosphorylated Ser12 (pS12) in complex with FBP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 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.444, T.445, K.446, T.447, R.449, S.450, W.495, R.502, G.527, W.528, R.529, P.530, G.531, S.532, G.533, Y.534, T.535 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.445, A:T.445, A:K.446, A:T.447, A:R.449, A:S.450, A:S.450, A:G.527, A:R.529, A:G.531, A:G.533, A:Y.534 Water bridges: A:W.495, A:R.502, A:R.502, A:R.502, A:R.502, A:G.527 Salt bridges: A:K.446, A:R.502 FBP.17: 17 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 Ligands: EDO.33 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:T.445, B:K.446, B:T.447, B:S.450, B:S.450, B:G.527, B:R.529, B:G.531, B:S.532, B:G.533, B:Y.534 Water bridges: B:K.446, B:T.447, B:R.502, B:R.502, B:G.527, B:T.535, B:T.535 Salt bridges: B:K.446, B:R.502 FBP.34: 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 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:T.445, C:K.446, C:T.447, C:R.449, C:S.450, C:G.527, C:R.529, C:G.531, C:S.532, C:G.533, C:Y.534 Water bridges: C:K.446, C:T.447, C:R.468, C:W.495, C:R.502, C:R.502, C:R.502, C:R.502, C:R.502, C:T.535, C:T.535 Salt bridges: C:K.446, C:R.502 FBP.47: 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 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:T.445, D:K.446, D:T.447, D:S.450, D:S.450, D:G.527, D:R.529, D:G.531, D:G.533, D:Y.534 Water bridges: D:K.446, D:K.446, D:R.449, D:W.495, D:R.502, D:R.502, D:R.502, D:G.527, D:T.535 Salt bridges: D:K.446, D:R.502

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

MG.2: 5 residues within 4Å: Chain A: E.285, D.309 Ligands: MG.5, ATP.6, OXL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.285, A:D.309 MG.3: 2 residues within 4Å: Chain A: D.191 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain A: N.88, S.90, D.126, T.127, S.256, K.283 Ligands: ATP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.90, A:D.126, A:T.127, H2O.2 MG.5: 6 residues within 4Å: Chain A: R.133, D.191, G.221, D.309 Ligands: MG.2, ATP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.309, A:D.309, H2O.3, H2O.9 MG.18: 4 residues within 4Å: Chain B: E.285, D.309 Ligands: ATP.22, OXL.23 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.285, B:D.309 MG.19: 6 residues within 4Å: Chain B: N.88, S.90, D.126, T.127, S.256 Ligands: ATP.22 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.90, B:D.126, B:T.127, H2O.18 MG.20: 2 residues within 4Å: Chain B: D.191 Ligands: ATP.22 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain B: R.133, D.191, G.221, D.309 Ligands: ATP.22 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.309, B:D.309, H2O.14, H2O.15 MG.35: 3 residues within 4Å: Chain C: E.285, D.309 Ligands: OXL.37 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.285, C:D.309 MG.36: 5 residues within 4Å: Chain C: N.88, S.90, D.126, T.127, S.256 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.90, C:D.126, C:T.127, H2O.28, H2O.29 MG.48: 1 residues within 4Å: Ligands: ATP.51 No protein-ligand interaction detected (PLIP) MG.49: 4 residues within 4Å: Chain D: E.285, D.309 Ligands: ATP.51, OXL.52 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.285, D:D.309 MG.50: 7 residues within 4Å: Chain D: N.88, S.90, D.126, T.127, S.256, K.283 Ligands: ATP.51 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.90, D:D.126, D:T.127, H2O.38

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

ATP.6: 24 residues within 4Å: Chain A: T.63, I.64, P.66, R.86, N.88, H.91, Y.96, H.97, D.126, R.133, D.191, K.220, K.283, D.309, S.375, G.376, A.379, K.380 Ligands: MG.2, MG.3, MG.4, MG.5, OXL.7, EDO.10 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:I.64, A:N.88, A:K.220, A:K.220, A:S.375 Water bridges: A:G.92, A:R.133, A:D.190, A:K.220, A:S.256, A:G.376, A:K.380 Salt bridges: A:R.86, A:R.86, A:H.91, A:R.133, A:R.133, A:K.283 pi-Stacking: A:H.91 ATP.22: 23 residues within 4Å: Chain B: T.63, I.64, P.66, R.86, N.88, H.91, Y.96, H.97, D.126, R.133, D.191, K.220, K.283, D.309, S.375, A.379, K.380 Ligands: MG.18, MG.19, MG.20, MG.21, OXL.23, PGE.24 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:I.64, B:N.88, B:K.220, B:K.220 Water bridges: B:R.86, B:R.86, B:R.133, B:R.133, B:R.133, B:D.190, B:S.256, B:G.376 Salt bridges: B:R.86, B:R.86, B:H.91, B:R.133, B:R.133, B:K.283 pi-Stacking: B:H.91 ATP.51: 21 residues within 4Å: Chain D: T.63, I.64, P.66, R.86, N.88, H.91, Y.96, H.97, D.126, R.133, K.220, K.283, D.309, S.375, A.379, K.380 Ligands: MG.48, MG.49, MG.50, OXL.52, EDO.54 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:I.64, D:N.88, D:D.126, D:K.220, D:K.220, D:S.375 Water bridges: D:R.133, D:R.133, D:R.133, D:D.190, D:D.190, D:D.190, D:G.376, D:K.380 Salt bridges: D:R.86, D:R.86, D:H.91, D:R.133, D:R.133, D:K.283 pi-Stacking: D:H.91

4 x OXL: OXALATE ION(Non-covalent)

OXL.7: 12 residues within 4Å: Chain A: R.86, K.283, E.285, M.304, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MG.2, ATP.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.285, A:E.285, A:G.308, A:D.309 Salt bridges: A:R.86, A:K.283, A:K.283 OXL.23: 12 residues within 4Å: Chain B: R.86, K.283, E.285, M.304, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MG.18, ATP.22 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.285, B:G.308, B:D.309, B:T.341, B:T.341 Water bridges: B:R.86 Salt bridges: B:R.86, B:K.283, B:K.283 OXL.37: 10 residues within 4Å: Chain C: R.86, K.283, E.285, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MG.35 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.308, C:D.309, C:T.341, C:T.341, C:T.341 Water bridges: C:R.86 Salt bridges: C:R.86, C:K.283, C:K.283 OXL.52: 12 residues within 4Å: Chain D: R.86, K.283, E.285, M.304, A.306, R.307, G.308, D.309, T.341, M.373 Ligands: MG.49, ATP.51 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.285, D:G.308, D:D.309 Salt bridges: D:R.86, D:K.283

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

EDO.8: 5 residues within 4Å: Chain A: A.55, R.56, H.392, F.483 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 10 residues within 4Å: Chain A: G.334, K.335, P.336, D.370, Q.452, S.455, Q.456, R.458, L.478, S.479 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: H.91, P.141, S.218, R.219, K.220 Ligands: ATP.6 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: R.56, K.79, A.80, G.81, R.119, H.392 Ligands: EDO.8 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.352, P.353, R.355 Chain B: D.191, G.192 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.70, V.71, D.72, N.103 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: N.249 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: N.249, S.469, A.470, Q.471, R.474 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: A.55, R.56, H.392, R.396 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain B: L.541 Chain D: W.528 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: R.73, S.382, F.383, P.384, V.385, E.386 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: V.222, N.223, L.224, V.229, E.313 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: H.404, R.405, F.408, F.434 Ligands: EDO.32 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: M.389, M.390, A.393 Chain B: E.317 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: E.431, F.434, K.435 Chain D: R.412, L.417, I.427 Ligands: EDO.30 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: R.468, P.491, W.495, D.498, R.502, P.530 Ligands: FBP.17 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: E.317 Chain D: M.389, M.390, A.393 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain C: R.56, K.79, A.80, G.81, R.119, H.392 Ligands: EDO.40 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain C: A.55, R.56, H.392, R.396, F.483 Ligands: EDO.39 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain C: R.352, P.353, R.355 Chain D: D.191, G.192 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain C: R.329 Chain D: C.44 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain C: T.63, R.86, N.88, H.91, S.375, A.379 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: D.301, K.335, P.336, Q.452 Ligands: EDO.45 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain C: R.268, E.298, V.299, S.300, D.301, K.335 Ligands: EDO.44 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain C: P.421, W.528, Y.534 Ligands: PG4.16 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain B: R.412 Chain D: R.405, F.408, R.412, F.434 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain D: H.91, P.141, S.218, R.219, K.220 Ligands: ATP.51 Ligand excluded by PLIP EDO.55: 9 residues within 4Å: Chain D: G.334, K.335, P.336, D.370, Q.452, S.455, Q.456, R.458, S.479 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain D: A.55, R.56, H.392 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain D: V.71, E.106 Ligands: PEG.61 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain D: P.66, A.67, R.69, S.70, R.73 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain D: N.249, S.469, A.470, Q.471, R.474 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain D: V.222, N.223, L.224, V.229, E.313 Ligand excluded by PLIP

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

PEG.15: 9 residues within 4Å: Chain A: V.402, H.404, R.458, P.459, A.461, A.462, V.463, R.480, G.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.463, A:R.480, A:G.481 PEG.61: 5 residues within 4Å: Chain D: S.70, V.71, D.72, N.103 Ligands: EDO.57 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.71, D:D.72, D:D.72

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 8 residues within 4Å: Chain A: R.539, V.540, L.541, S.542 Chain C: P.421, W.528, N.536 Ligands: EDO.46 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.539, A:S.542, A:S.542, C:N.536

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

PGE.24: 8 residues within 4Å: Chain B: H.91, G.92, P.141, E.142, S.218, R.219, K.220 Ligands: ATP.22 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.91, B:G.92, B:E.142, B:S.218, B:R.219, B:K.220

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.62: 1 residues within 4Å: Chain D: G.213 Ligand excluded by PLIP

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
C

D
D

Pyruvate kinase PKLR

Related Entries With Identical Sequence