SMTL ID : 1t5a.2 (1 other biounit)

Human Pyruvate Kinase M2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 15 residues within 4Å: Chain A: L.467, T.468, K.469, S.470, S.473, W.518, R.525, G.550, R.552, P.553, G.554, S.555, G.556, F.557, T.558 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.468, A:T.468, A:K.469, A:S.470, A:S.473, A:S.473, A:S.473, A:G.550, A:R.552, A:G.554, A:G.556, A:F.557, A:T.558 Water bridges: A:T.558 Salt bridges: A:K.469, A:R.525 FBP.11: 16 residues within 4Å: Chain B: L.467, T.468, K.469, S.470, R.472, S.473, W.518, R.525, G.550, R.552, P.553, G.554, S.555, G.556, F.557, T.558 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.468, B:K.469, B:S.470, B:G.471, B:S.473, B:S.473, B:S.473, B:G.550, B:G.550, B:R.552, B:G.554, B:G.556, B:F.557 Water bridges: B:T.558 Salt bridges: B:K.469, B:R.472, B:R.525 FBP.22: 17 residues within 4Å: Chain C: L.467, T.468, K.469, S.470, G.471, R.472, S.473, W.518, R.525, G.550, R.552, P.553, G.554, S.555, G.556, F.557, T.558 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.468, C:T.468, C:K.469, C:S.470, C:G.471, C:S.473, C:S.473, C:S.473, C:G.550, C:G.550, C:G.554, C:G.556, C:F.557, C:T.558 Water bridges: C:T.558 Salt bridges: C:K.469, C:R.472, C:R.525 FBP.31: 17 residues within 4Å: Chain D: L.467, T.468, K.469, S.470, G.471, R.472, S.473, W.518, R.525, G.550, R.552, P.553, G.554, S.555, G.556, F.557, T.558 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.468, D:T.468, D:K.469, D:S.470, D:G.471, D:S.473, D:S.473, D:S.473, D:G.550, D:G.550, D:R.552, D:G.554, D:G.556, D:F.557, D:T.558 Salt bridges: D:K.469, D:R.472, D:R.525

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: K.306, E.308, A.329, R.330, G.331, D.332, T.364, M.396 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.308, A:G.331, A:D.332, A:T.364, A:T.364 Water bridges: A:K.306 Salt bridges: A:R.109, A:K.306, A:K.306 OXL.12: 7 residues within 4Å: Chain B: K.306, E.308, A.329, G.331, D.332, T.364 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.331, B:D.332, B:T.364, B:T.364 Salt bridges: B:R.109, B:K.306, B:K.306 OXL.23: 9 residues within 4Å: Chain C: K.306, E.308, A.329, R.330, G.331, D.332, T.364, M.396 Ligands: MG.25 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.331, C:D.332, C:T.364 Water bridges: C:R.109 Salt bridges: C:R.109, C:K.306, C:K.306 OXL.32: 8 residues within 4Å: Chain D: K.306, E.308, A.329, R.330, G.331, D.332, T.364 Ligands: MG.34 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.308, D:E.308, D:G.331, D:D.332, D:D.332, D:T.364, D:T.364 Water bridges: D:R.109 Salt bridges: D:R.109, D:K.306, D:K.306

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: N.111, S.113, H.114, R.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.111, A:S.113 Salt bridges: A:H.114, A:R.156 PO4.13: 3 residues within 4Å: Chain B: N.111, H.114, R.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.111 Salt bridges: B:H.114, B:R.156 PO4.24: 3 residues within 4Å: Chain C: N.111, H.114, R.156 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.111 Salt bridges: C:H.114, C:R.156 PO4.33: 3 residues within 4Å: Chain D: N.111, H.114, R.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.111 Salt bridges: D:H.114, D:R.156

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.308, D.332 Ligands: OXL.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.308, A:D.332, H2O.1 MG.14: 4 residues within 4Å: Chain B: K.306, E.308, D.332 Ligands: OXL.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.308, B:D.332 MG.25: 4 residues within 4Å: Chain C: K.306, E.308, D.332 Ligands: OXL.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.308, C:D.332 MG.34: 3 residues within 4Å: Chain D: E.308, D.332 Ligands: OXL.32 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.308, D:D.332

4 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: N.111, S.113, D.149, T.150, S.279, K.306 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain B: N.111, S.113, D.149, T.150 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.149 K.26: 5 residues within 4Å: Chain C: N.111, S.113, D.149, T.150, S.279 No protein-ligand interaction detected (PLIP) K.35: 6 residues within 4Å: Chain D: N.111, S.113, D.149, T.150, E.154, S.279 No protein-ligand interaction detected (PLIP)

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: H.114, G.115, K.242 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: W.518, A.519, D.523, T.549, G.550 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: P.153, E.154, I.155, V.252, F.280, E.336 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.79, K.102, S.103, G.104, R.142, N.415 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: E.321, S.323, D.324, K.358 Chain C: K.161, S.163, A.166 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: H.114, G.115, K.242 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: W.518, D.523, T.549, R.562 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: P.153, V.245, N.246, L.247, V.252, F.280, E.336 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain B: C.353, N.354, G.357, K.358, D.393, R.479, R.481, Y.502 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: R.79, K.102, S.103, G.104, R.142, N.415, R.536 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain B: R.291, E.321, A.322, S.323, D.324, K.358 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: H.114, G.115, K.242 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: W.518, A.519, V.522, D.523, G.550 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: R.79, K.102, S.103, R.142, N.415, R.536 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain C: R.291, E.321, A.322, D.324, K.358 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain D: H.114, G.115, K.242 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain D: V.522, D.523, T.549, G.550, R.562 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: P.153, V.245, N.246, L.247, V.252, F.280, E.336 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain D: R.79, K.102, S.103, G.104, R.142, N.415 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain D: R.291, E.321, A.322, S.323, D.324, K.358 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dombrauckas, J.D. et al., Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis. Biochemistry (2005)

Release Date

2005-07-12

Peptides

Pyruvate kinase, M2 isozyme: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Pyruvate kinase, M2 isozyme

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