SMTL ID : 3gqy.1

Activator-Bound Structure of Human Pyruvate Kinase M2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.452, A:S.453, A:G.454, A:S.456, 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:R.474, A:R.508, A:T.541 Salt bridges: A:R.508 FBP.5: 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 20 PLIP interactions: 20 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: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:R.508, B:T.541 Salt bridges: B:K.452, B:R.508 FBP.12: 8 residues within 4Å: Chain C: L.450, T.451, K.452, S.453, G.454, R.455, S.456, T.541 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456 FBP.16: 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: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:R.508, D:R.508, D:T.541 Salt bridges: D:K.452, D:R.508

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

TLA.2: 11 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.3 13 PLIP interactions: 13 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:S.96, A:E.137, A:S.262, A:K.289 Salt bridges: A:R.92, A:K.289 TLA.6: 9 residues within 4Å: Chain B: R.92, D.132, K.289, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.10 12 PLIP interactions: 12 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:N.94, B:S.96, B:S.262 Salt bridges: B:R.92, B:K.289 TLA.7: 6 residues within 4Å: Chain B: G.232, A.233, A.234, H.293, E.294, R.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.233 Water bridges: B:G.232 Salt bridges: B:H.293 TLA.13: 9 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.289, C:E.291, C:G.314, C:D.315, C:D.315, C:D.315 Water bridges: C:N.94, C:S.96, C:E.137 Salt bridges: C:R.92, C:K.289 TLA.17: 8 residues within 4Å: Chain D: R.92, K.289, A.312, R.313, G.314, D.315, T.347 Ligands: UNX.21 10 PLIP interactions: 10 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.381, D:S.381 Salt bridges: D:R.92, D:K.289 TLA.18: 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

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

UNX.3: 7 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.2 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain B: K.280, K.282, N.283 No protein-ligand interaction detected (PLIP) UNX.9: 5 residues within 4Å: Chain B: N.63, H.483, Y.485, G.487, I.488 No protein-ligand interaction detected (PLIP) UNX.10: 7 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.6 No protein-ligand interaction detected (PLIP) UNX.14: 5 residues within 4Å: Chain C: G.147, T.148, A.149, G.223, S.224 No protein-ligand interaction detected (PLIP) UNX.15: 7 residues within 4Å: Chain C: N.94, S.96, D.132, T.133, S.262, K.289 Ligands: TLA.13 No protein-ligand interaction detected (PLIP) UNX.19: 3 residues within 4Å: Chain D: K.108, R.111, T.112 No protein-ligand interaction detected (PLIP) UNX.20: 3 residues within 4Å: Chain D: K.81, S.116, F.117 No protein-ligand interaction detected (PLIP) UNX.21: 7 residues within 4Å: Chain D: R.92, N.94, S.96, D.132, T.133, K.289 Ligands: TLA.17 No protein-ligand interaction detected (PLIP)

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

DZG.4: 19 residues within 4Å: Chain A: F.45, L.46, M.49, N.337, D.373, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.45, A:L.413 pi-Stacking: A:F.45, B:F.45 pi-Cation interactions: A:F.45, B:F.45 DZG.11: 19 residues within 4Å: Chain C: F.45, L.46, M.49, N.337, D.373, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, M.49, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.45, D:L.413 pi-Stacking: D:F.45, C:F.45 pi-Cation interactions: D:F.45, C: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

2009-04-07

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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