SMTL ID : 3h6o.1

Activator-Bound Structure of Human Pyruvate Kinase M2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 Ligands: UNX.11 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.452, A:S.453, A:S.456, A:S.456, A:S.456, A:G.533, A:R.535, A:G.537, A:S.538, A:G.539, A:F.540 Salt bridges: A:K.452, A:R.508 FBP.14: 17 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 Ligands: UNX.20 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.452, B:S.453, B:G.454, B:S.456, B:S.456, B:S.456, B:G.533, B:R.535, B:G.537, B:S.538, B:G.539, B:F.540 Water bridges: B:R.455, B:R.455, B:R.508, B:R.508 Salt bridges: B:K.452, B:R.508 FBP.24: 17 residues within 4Å: Chain C: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456, C:S.456, C:G.533, C:R.535, C:R.535, C:G.537, C:S.538, C:G.539, C:F.540 Salt bridges: C:K.452, C:R.508 FBP.30: 17 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 Ligands: UNX.34 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.451, D:K.452, D:S.453, D:G.454, D:R.455, D:S.456, D:S.456, D:G.533, D:R.535, D:R.535, D:G.537, D:S.538, D:G.539, D:F.540 Water bridges: D:L.450 Salt bridges: D:K.452, D:R.508

31 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 3 residues within 4Å: Chain A: R.92, N.94, S.381 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: I.245, K.249, V.276 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: K.108, R.111, T.112 Ligand excluded by PLIP UNX.5: 4 residues within 4Å: Chain A: E.82, K.85, S.86, R.395 Ligand excluded by PLIP UNX.6: 5 residues within 4Å: Chain A: C.336, N.337, K.341, D.376, R.464 Ligand excluded by PLIP UNX.7: 5 residues within 4Å: Chain A: D.255, V.256, D.257, Q.477, R.480 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: Q.329, D.366, N.369, A.370 Chain B: S.365 Ligand excluded by PLIP UNX.9: 7 residues within 4Å: Chain A: R.92, N.94, S.96, D.132, T.133, S.262, K.289 Ligand excluded by PLIP UNX.10: 5 residues within 4Å: Chain A: K.266, A.267, S.268, R.298, E.301 Ligand excluded by PLIP UNX.11: 6 residues within 4Å: Chain A: T.428, S.456, G.539, F.540, T.541 Ligands: FBP.1 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: E.291, G.314, D.315 Ligand excluded by PLIP UNX.15: 6 residues within 4Å: Chain B: R.92, N.94, S.96, D.132, T.133, K.289 Ligand excluded by PLIP UNX.16: 8 residues within 4Å: Chain B: Y.194, V.195, D.196, D.197, G.198, G.227, V.228, N.229 Ligand excluded by PLIP UNX.17: 7 residues within 4Å: Chain B: M.353, I.354, E.383, G.387, D.388, Y.389, P.390 Ligand excluded by PLIP UNX.18: 7 residues within 4Å: Chain A: N.369 Chain B: Q.329, K.330, N.369, A.370, D.373 Ligands: UNX.21 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain B: E.291, D.315 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain B: S.456, G.539, F.540, T.541 Ligands: FBP.14 Ligand excluded by PLIP UNX.21: 6 residues within 4Å: Chain A: S.365 Chain B: R.313, Q.329, D.366, A.370 Ligands: UNX.18 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain B: A.312, R.313, G.314, D.315, T.347 Ligand excluded by PLIP UNX.23: 7 residues within 4Å: Chain B: T.347, Q.348, M.349, M.379, L.380, S.381, E.383 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain C: S.439, F.440, R.466, A.467 Ligand excluded by PLIP UNX.27: 8 residues within 4Å: Chain C: Y.194, V.195, D.196, D.197, G.198, G.227, V.228, N.229 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain C: A.312, D.315, T.347 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain C: A.500, W.501 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain D: G.340, R.462, R.464 Ligand excluded by PLIP UNX.32: 7 residues within 4Å: Chain D: T.347, Q.348, M.349, M.379, L.380, S.381, E.383 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Ligands: D8G.25 Ligand excluded by PLIP UNX.34: 6 residues within 4Å: Chain D: T.428, S.456, G.539, F.540, T.541 Ligands: FBP.30 Ligand excluded by PLIP UNX.35: 5 residues within 4Å: Chain C: L.327 Chain D: Q.36, S.56, E.403, A.406 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain D: T.347 Ligands: UNX.37 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain D: E.291, D.315 Ligands: UNX.36 Ligand excluded by PLIP

2 x D8G: 6-(2-fluorobenzyl)-2,4-dimethyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one(Non-covalent)

D8G.13: 11 residues within 4Å: Chain A: F.45, L.372, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, Y.409, Q.412, L.413 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.45, A:L.413, B:L.46, B:L.413 pi-Stacking: A:F.45, B:F.45, B:F.45, B:F.45 D8G.25: 12 residues within 4Å: Chain C: F.45, L.372, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, Y.409, Q.412, L.413 Ligands: UNX.33 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.45, C:F.45, C:L.413, C:L.413, D:L.46, D:Y.409, D:L.413 pi-Stacking: C:F.45, D:F.45, D:F.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, B. et al., Activator-Bound Structures of Human Pyruvate Kinase M2. to be published

Release Date

2009-05-05

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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