SMTL ID : 3gr4.1

Activator-Bound Structure of Human Pyruvate Kinase M2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, W.534, R.535, P.536, G.537, S.538, G.539, F.540, T.541 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.452, A:S.453, A:G.454, A:S.456, A:S.456, A:G.533, A:R.535, A:R.535, A:G.537, A:S.538, A:G.539, A:F.540 Water bridges: A:D.504, A:R.508, A:R.508 Salt bridges: A:R.508 FBP.11: 16 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.452, B:S.453, 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, B:T.541 Salt bridges: B:K.452, B:R.508 FBP.20: 6 residues within 4Å: Chain C: T.451, K.452, S.453, R.455, S.456, T.541 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:S.456, C:S.456, C:S.456, C:T.541 FBP.26: 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 22 PLIP interactions: 22 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:R.535, D:G.537, D:S.538, D:G.539, D:F.540 Water bridges: D:K.452, D:R.455, D:R.455, D:R.508, D:R.508, D:T.541 Salt bridges: D:K.452, D:R.508

7 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 12 residues within 4Å: Chain A: R.92, N.94, D.132, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.4, ADP.10 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.94, A:K.289, A:K.289, A:G.314, A:D.315, A:T.347 Water bridges: A:S.96, A:E.137, A:S.262, A:K.289 Salt bridges: A:R.92, A:K.289 TLA.12: 9 residues within 4Å: Chain B: R.92, D.132, K.289, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.14 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.289, B:K.289, B:G.314, B:D.315, B:D.315, B:T.347 Water bridges: B:N.94, B:S.96, B:S.96, B:S.262, B:K.289, B:D.315 Salt bridges: B:R.92, B:K.289 TLA.19: 6 residues within 4Å: Chain B: G.232, A.233, A.234, H.293, E.294, R.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.233 Salt bridges: B:H.293 TLA.21: 8 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.289, C:E.291, C:E.291, C:G.314, C:D.315, C:D.315 Water bridges: C:S.96, C:S.262 Salt bridges: C:R.92, C:K.289 TLA.24: 7 residues within 4Å: Chain C: G.71, P.72, N.94, H.97, Y.102, A.385, K.386 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.97, C:Y.102, C:Y.102, C:A.385 Water bridges: C:N.94 TLA.27: 9 residues within 4Å: Chain D: R.92, D.132, K.289, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.30 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.289, D:K.289, D:G.314, D:D.315, D:D.315 Water bridges: D:S.96, D:S.262, D:S.381, D:S.381 Salt bridges: D:R.92, D:K.289 TLA.32: 6 residues within 4Å: Chain D: G.232, A.233, A.234, H.293, E.294, R.297 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.233 Water bridges: D:H.293, D:E.294 Salt bridges: D:H.293

2 x DYY: 1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine(Non-covalent)

DYY.3: 17 residues within 4Å: Chain A: F.45, L.46, M.49, L.372, Y.409, Q.412, L.413, E.416 Chain B: F.45, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.413, A:F.45, A:L.413 pi-Stacking: B:F.45, A:F.45 pi-Cation interactions: B:F.45, A:F.45 DYY.25: 17 residues within 4Å: Chain C: F.45, L.46, M.49, L.372, Y.409, Q.412, L.413, E.416 Chain D: F.45, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.413, D:F.45, D:L.413 Water bridges: C:Y.409 pi-Stacking: C:F.45 pi-Cation interactions: C:F.45, D:F.45 Hydrogen bonds: D:Y.409

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

UNX.4: 7 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.2 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: R.62, G.87, H.398 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: T.133, K.134, D.244, D.247 Ligand excluded by PLIP UNX.7: 5 residues within 4Å: Chain A: C.336, N.337, K.341, D.376, R.464 Ligand excluded by PLIP UNX.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: R.298, D.300, E.301 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain B: P.72, R.75 Ligand excluded by PLIP UNX.14: 7 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.12 Ligand excluded by PLIP UNX.15: 5 residues within 4Å: Chain B: M.88, N.89, R.125, P.126, H.483 Ligand excluded by PLIP UNX.16: 4 residues within 4Å: Chain B: N.63, H.483, Y.485, I.488 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain B: R.464, P.465, R.486 Ligand excluded by PLIP UNX.18: 1 residues within 4Å: Chain B: S.538 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain C: T.451, K.452, T.473, R.474 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain C: H.100, K.243, Q.246, D.247 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain D: R.111, R.480 Ligands: UNX.29 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain D: R.111, D.255, D.257, R.480 Ligands: UNX.28 Ligand excluded by PLIP UNX.30: 8 residues within 4Å: Chain D: R.92, N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.27 Ligand excluded by PLIP UNX.31: 7 residues within 4Å: Chain D: M.353, I.354, E.383, G.387, D.388, Y.389, P.390 Ligand excluded by PLIP

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.10: 10 residues within 4Å: Chain A: T.69, G.71, P.72, R.92, N.94, H.97, R.139, S.381, A.385 Ligands: TLA.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.94, A:N.94, A:H.97, A:S.381 Water bridges: A:N.94, A:R.139, A:R.139, A:S.381, A:G.382 Salt bridges: A:R.92, A:H.97, A:R.139

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

2009-04-07

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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