SMTL ID : 4b5t.1

Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with ketobutyrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-hexamer

Ligands

6 x CO: COBALT (II) ION(Non-covalent)

CO.1: 7 residues within 4Å: Chain A: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.4, 2KT.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, H2O.5, H2O.5 CO.6: 7 residues within 4Å: Chain B: H.45, R.70, Q.147, E.149, D.175 Ligands: MG.7, 2KT.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, H2O.21, H2O.21 CO.10: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.13, 2KT.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, H2O.36, H2O.36 CO.15: 7 residues within 4Å: Chain D: H.45, R.70, Q.147, E.149, D.175 Ligands: MG.16, 2KT.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, H2O.52, H2O.53 CO.19: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.22, 2KT.23 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, H2O.68, H2O.68 CO.24: 7 residues within 4Å: Chain F: H.45, R.70, Q.147, E.149, D.175 Ligands: MG.25, 2KT.27 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.84, H2O.84

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: S.24, S.25, Y.26 Chain B: L.22, S.23, S.24, P.47 Chain D: Q.51, L.54, T.55 Ligands: GOL.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.25, A:S.25, A:S.25, A:Y.26, D:Q.51 Water bridges: A:S.24, A:S.25, A:S.27 GOL.3: 10 residues within 4Å: Chain A: L.22, S.23, S.24, P.47 Chain B: S.24, S.25, Y.26 Chain E: L.54, T.55 Ligands: GOL.2 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.25, B:Y.26 Water bridges: B:S.25, B:S.25, B:S.25, B:S.25, B:S.27, A:L.22 GOL.8: 8 residues within 4Å: Chain B: M.154, K.155, L.157, P.158, A.194, Q.197, A.198, Q.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.154, B:M.154, B:Q.197 Water bridges: B:Q.197 GOL.11: 11 residues within 4Å: Chain C: S.24, S.25, Y.26 Chain D: L.22, S.23, S.24, P.47 Chain F: Q.51, L.54, T.55 Ligands: GOL.12 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain C Hydrogen bonds: F:Q.51, C:S.25, C:S.25, C:S.25, C:Y.26 Water bridges: C:S.24, C:S.25, C:S.27 GOL.12: 10 residues within 4Å: Chain A: L.54, T.55 Chain C: L.22, S.23, S.24, P.47 Chain D: S.24, S.25, Y.26 Ligands: GOL.11 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Water bridges: C:L.22, D:S.25, D:S.25, D:S.25, D:S.25, D:S.27 Hydrogen bonds: D:S.25, D:Y.26 GOL.17: 8 residues within 4Å: Chain D: M.154, K.155, L.157, P.158, A.194, Q.197, A.198, Q.201 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:M.154, D:M.154, D:Q.197 Water bridges: D:Q.197 GOL.20: 11 residues within 4Å: Chain B: Q.51, L.54, T.55 Chain E: S.24, S.25, Y.26 Chain F: L.22, S.23, S.24, P.47 Ligands: GOL.21 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.25, E:S.25, E:S.25, E:Y.26, B:Q.51 Water bridges: E:S.24, E:S.25, E:S.27 GOL.21: 10 residues within 4Å: Chain C: L.54, T.55 Chain E: L.22, S.23, S.24, P.47 Chain F: S.24, S.25, Y.26 Ligands: GOL.20 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.25, F:Y.26 Water bridges: F:S.25, F:S.25, F:S.25, F:S.25, F:S.27, E:L.22 GOL.26: 8 residues within 4Å: Chain F: M.154, K.155, L.157, P.158, A.194, Q.197, A.198, Q.201 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:M.154, F:M.154, F:Q.197 Water bridges: F:Q.197

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.1, 2KT.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, H2O.5, H2O.5 MG.7: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.6, 2KT.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, H2O.21, H2O.21 MG.13: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.10, 2KT.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, H2O.36, H2O.36 MG.16: 7 residues within 4Å: Chain D: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.15, 2KT.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, H2O.52, H2O.53 MG.22: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.19, 2KT.23 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, H2O.68, H2O.68 MG.25: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.24, 2KT.27 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.84, H2O.84

6 x 2KT: 2-KETOBUTYRIC ACID(Non-covalent)

2KT.5: 12 residues within 4Å: Chain A: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.1, MG.4 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain A Water bridges: E:V.118, A:R.70, A:R.70 Hydrophobic interactions: A:W.19, A:F.170, A:F.170, A:L.212 Hydrogen bonds: A:R.70, A:Q.147, A:A.174, A:D.175 2KT.9: 12 residues within 4Å: Chain B: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.6, MG.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.19, B:F.170, B:F.170, B:L.212, B:L.212 Hydrogen bonds: B:R.70, B:R.70, B:Q.147, B:A.174, B:D.175 2KT.14: 12 residues within 4Å: Chain C: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.10, MG.13 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.19, C:F.170, C:F.170, C:L.212 Hydrogen bonds: C:R.70, C:Q.147, C:A.174, C:D.175 Water bridges: C:R.70, C:R.70, A:V.118 2KT.18: 12 residues within 4Å: Chain D: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.15, MG.16 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.19, D:F.170, D:F.170, D:L.212, D:L.212 Hydrogen bonds: D:R.70, D:R.70, D:Q.147, D:A.174, D:D.175 2KT.23: 12 residues within 4Å: Chain E: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.19, MG.22 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain E Water bridges: C:V.118, E:R.70, E:R.70 Hydrophobic interactions: E:W.19, E:F.170, E:F.170, E:L.212 Hydrogen bonds: E:R.70, E:Q.147, E:A.174, E:D.175 2KT.27: 12 residues within 4Å: Chain F: W.19, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.24, MG.25 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:W.19, F:F.170, F:F.170, F:L.212, F:L.212 Hydrogen bonds: F:R.70, F:R.70, F:Q.147, F:A.174, F:D.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coincon, M. et al., Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity. J.Biol.Chem. (2012)

Release Date

2012-08-29

Peptides

4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE

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