SMTL ID : 3me3.1

Activator-Bound Structure of Human Pyruvate Kinase M2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x 3SZ: 3-{[4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-1,4-diazepan-1-yl]sulfonyl}aniline(Non-covalent)

3SZ.1: 17 residues within 4Å: Chain A: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, M.49, L.372, D.373, Y.409, Q.412, L.413, E.416 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.45, B:L.413, A:F.45 Hydrogen bonds: B:L.372 Water bridges: B:Y.409 pi-Stacking: B:F.45 pi-Cation interactions: B:F.45, A:F.45 3SZ.43: 16 residues within 4Å: Chain C: F.45, L.46, L.372, D.373, Y.409, Q.412, L.413, E.416 Chain D: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.413, C:F.45, C:L.413 pi-Stacking: D:F.45, C:F.45 pi-Cation interactions: D:F.45, C:F.45 Hydrogen bonds: C:L.372

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

FBP.2: 18 residues within 4Å: Chain A: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, T.532, G.533, W.534, R.535, P.536, G.537, S.538, G.539, F.540, T.541 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.452, A:S.453, A:S.456, A:S.456, A:G.533, A:R.535, A:G.537, A:S.538, A:G.539, A:F.540 Water bridges: A:D.504, A:D.504, A:R.508 Salt bridges: A:K.452, A:R.508 FBP.18: 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.22 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: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.474, B:R.508, B:R.508 Salt bridges: B:K.452, B:R.508 FBP.30: 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 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:S.456, C:S.456, C:G.533, C:G.537, C:S.538, C:G.539, C:F.540, C:T.541 Water bridges: C:R.508, C:R.508, C:R.508, C:T.541 Salt bridges: C:K.452, C:R.508 FBP.44: 17 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, W.534, R.535, P.536, G.537, S.538, G.539, F.540, T.541 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.451, D:K.452, D:S.453, D:R.455, D:S.456, D:S.456, D:S.456, D:G.533, D:R.535, D:G.537, D:S.538, D:G.539, D:F.540 Water bridges: D:R.508, D:R.508, D:T.541 Salt bridges: D:K.452, D:R.508

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: S.96, H.97, G.98, K.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.98 Salt bridges: A:H.97 SO4.19: 6 residues within 4Å: Chain B: R.92, N.94, S.96, D.132, K.289 Ligands: UNX.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.94, B:S.96 Water bridges: B:R.92 Salt bridges: B:R.92, B:K.289 SO4.31: 2 residues within 4Å: Chain C: V.497, E.499 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.499 SO4.45: 6 residues within 4Å: Chain D: R.92, N.94, S.96, D.132, K.289 Ligands: UNX.50 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.94, D:S.96 Salt bridges: D:R.92, D:K.289

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

UNX.4: 3 residues within 4Å: Chain A: R.62, G.87, H.398 Ligand excluded by PLIP UNX.5: 9 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: UNX.8, UNX.9, UNX.10 Ligand excluded by PLIP UNX.6: 7 residues within 4Å: Chain A: S.262, F.263, K.289, E.291, D.315 Ligands: UNX.10, UNX.13 Ligand excluded by PLIP UNX.7: 6 residues within 4Å: Chain A: E.291, A.312, G.314, D.315, T.347 Ligands: UNX.13 Ligand excluded by PLIP UNX.8: 6 residues within 4Å: Chain A: R.92, N.94, K.289 Ligands: UNX.5, UNX.9, UNX.13 Ligand excluded by PLIP UNX.9: 6 residues within 4Å: Chain A: N.94, S.96, E.137, R.139 Ligands: UNX.5, UNX.8 Ligand excluded by PLIP UNX.10: 8 residues within 4Å: Chain A: S.96, T.133, K.134, E.137, S.262, F.263 Ligands: UNX.5, UNX.6 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: R.297 Ligand excluded by PLIP UNX.12: 1 residues within 4Å: Chain A: D.255 Ligand excluded by PLIP UNX.13: 6 residues within 4Å: Chain A: K.289, E.291, A.312 Ligands: UNX.6, UNX.7, UNX.8 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: E.82, K.85, S.86, R.395 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: I.245, K.249, V.276 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: R.111, Q.254 Ligand excluded by PLIP UNX.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain B: R.111 Ligand excluded by PLIP UNX.21: 7 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: SO4.19 Ligand excluded by PLIP UNX.22: 6 residues within 4Å: Chain B: T.428, S.456, G.539, F.540, T.541 Ligands: FBP.18 Ligand excluded by PLIP UNX.23: 5 residues within 4Å: Chain A: T.360, A.362 Chain B: Q.348, E.351, E.363 Ligand excluded by PLIP UNX.24: 6 residues within 4Å: Chain B: C.336, N.337, K.341, V.343, D.376, R.464 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain B: A.104, K.108, Q.254 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: T.360 Chain B: E.351, S.352, E.363 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain B: R.274, K.282 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain B: T.99, H.100 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain B: F.95, S.96, H.97, G.98, K.243 Ligand excluded by PLIP UNX.32: 8 residues within 4Å: Chain C: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: UNX.33, UNX.36 Ligand excluded by PLIP UNX.33: 9 residues within 4Å: Chain C: S.96, T.133, K.134, E.137, S.262, F.263 Ligands: UNX.32, UNX.34, UNX.36 Ligand excluded by PLIP UNX.34: 7 residues within 4Å: Chain C: S.262, F.263, K.289, E.291, D.315 Ligands: UNX.33, UNX.36 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain C: A.312, R.313, G.314, T.347 Ligand excluded by PLIP UNX.36: 5 residues within 4Å: Chain C: R.92, K.289 Ligands: UNX.32, UNX.33, UNX.34 Ligand excluded by PLIP UNX.37: 1 residues within 4Å: Chain C: R.139 Ligand excluded by PLIP UNX.38: 5 residues within 4Å: Chain C: G.147, T.148, A.149, G.223, S.224 Ligand excluded by PLIP UNX.39: 5 residues within 4Å: Chain C: N.63, H.483, Y.485, G.487, I.488 Ligand excluded by PLIP UNX.40: 1 residues within 4Å: Chain C: H.100 Ligand excluded by PLIP UNX.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.42: 4 residues within 4Å: Chain C: L.230, A.233, V.235, E.319 Ligand excluded by PLIP UNX.46: 4 residues within 4Å: Chain D: R.111, Q.254 Ligands: UNX.47, UNX.49 Ligand excluded by PLIP UNX.47: 6 residues within 4Å: Chain D: I.107, R.111, Q.254 Ligands: UNX.46, UNX.49, UNX.51 Ligand excluded by PLIP UNX.48: 2 residues within 4Å: Ligands: UNX.49, UNX.51 Ligand excluded by PLIP UNX.49: 4 residues within 4Å: Chain D: R.111 Ligands: UNX.46, UNX.47, UNX.48 Ligand excluded by PLIP UNX.50: 7 residues within 4Å: Chain D: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: SO4.45 Ligand excluded by PLIP UNX.51: 3 residues within 4Å: Chain D: K.108 Ligands: UNX.47, UNX.48 Ligand excluded by PLIP UNX.52: 5 residues within 4Å: Chain D: A.312, R.313, G.314, A.346, T.347 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anastasiou, D. et al., Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nat.Chem.Biol. (2012)

Release Date

2010-04-28

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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