SMTL ID : 4b5u.1

Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with pyruvate and succinic semialdehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 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.2, PYR.4 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, PYR.4, H2O.5, H2O.6 CO.6: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.7, PYR.9 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, PYR.9, H2O.17, H2O.21 CO.11: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.12, PYR.14 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, PYR.14, H2O.36, H2O.37 CO.16: 7 residues within 4Å: Chain D: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.17, PYR.19 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, PYR.19, H2O.48, H2O.52 CO.21: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.22, PYR.24 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, PYR.24, H2O.67, H2O.68 CO.26: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: MG.27, PYR.29 5 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, PYR.29, H2O.79, H2O.83

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.1, PYR.4 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, PYR.4, H2O.5, H2O.6 MG.7: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.6, PYR.9 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, PYR.9, H2O.17, H2O.21 MG.12: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.11, PYR.14 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, PYR.14, H2O.36, H2O.37 MG.17: 7 residues within 4Å: Chain D: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.16, PYR.19 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, PYR.19, H2O.48, H2O.52 MG.22: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.21, PYR.24 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, PYR.24, H2O.67, H2O.68 MG.27: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.26, PYR.29 5 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, PYR.29, H2O.79, H2O.83

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.8 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Q.51, A:S.24 Water bridges: A:S.25, A:S.27 GOL.8: 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.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.24, B:S.25 Water bridges: B:S.25, B:S.25, B:S.27 GOL.13: 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.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:S.24, F:Q.51 Water bridges: C:S.25, C:S.27 GOL.18: 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.13 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.24, D:S.25 Water bridges: D:S.25, D:S.25, D:S.27 GOL.23: 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.28 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.24, B:Q.51 Water bridges: E:S.25, E:S.27 GOL.28: 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.23 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.24, F:S.25 Water bridges: F:S.25, F:S.25, F:S.27

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 12 residues within 4Å: Chain A: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.1, MG.2, SSN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.170, A:L.212 Hydrogen bonds: A:R.70, A:R.70, A:Q.147, A:A.174, A:D.175 Water bridges: A:L.212 PYR.9: 12 residues within 4Å: Chain B: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.6, MG.7, SSN.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.170, B:L.212 Hydrogen bonds: B:R.70, B:R.70, B:Q.147, B:A.174, B:D.175 Water bridges: B:L.212 PYR.14: 12 residues within 4Å: Chain C: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.11, MG.12, SSN.15 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.170, C:L.212 Hydrogen bonds: C:R.70, C:R.70, C:Q.147, C:A.174, C:D.175 Water bridges: C:L.212 PYR.19: 12 residues within 4Å: Chain D: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.16, MG.17, SSN.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.170, D:L.212 Hydrogen bonds: D:R.70, D:R.70, D:Q.147, D:A.174, D:D.175 Water bridges: D:L.212 PYR.24: 12 residues within 4Å: Chain E: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.21, MG.22, SSN.25 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.170, E:L.212 Hydrogen bonds: E:R.70, E:R.70, E:Q.147, E:A.174, E:D.175 Water bridges: E:L.212 PYR.29: 12 residues within 4Å: Chain F: R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.26, MG.27, SSN.30 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.170, F:L.212 Hydrogen bonds: F:R.70, F:R.70, F:Q.147, F:A.174, F:D.175 Water bridges: F:L.212

6 x SSN: 4-oxobutanoic acid(Non-covalent)

SSN.5: 10 residues within 4Å: Chain A: W.19, H.45, R.70, A.174, L.212 Chain E: V.118, G.119, S.120, A.121 Ligands: PYR.4 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:R.70, A:R.70, E:S.120, E:A.121 Water bridges: A:A.174, E:N.129, E:N.129 SSN.10: 9 residues within 4Å: Chain B: H.45, R.70, A.174, L.212 Chain D: V.118, G.119, S.120, A.121 Ligands: PYR.9 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.121 Hydrogen bonds: D:S.120, D:A.121, B:R.70, B:R.70 Water bridges: D:N.129, B:A.174 SSN.15: 10 residues within 4Å: Chain A: V.118, G.119, S.120, A.121 Chain C: W.19, H.45, R.70, A.174, L.212 Ligands: PYR.14 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.120, A:A.121, C:R.70, C:R.70 Water bridges: A:N.129, A:N.129, C:A.174 SSN.20: 9 residues within 4Å: Chain D: H.45, R.70, A.174, L.212 Chain F: V.118, G.119, S.120, A.121 Ligands: PYR.19 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:A.121 Hydrogen bonds: F:S.120, F:A.121, D:R.70, D:R.70 Water bridges: F:N.129, D:A.174 SSN.25: 10 residues within 4Å: Chain C: V.118, G.119, S.120, A.121 Chain E: W.19, H.45, R.70, A.174, L.212 Ligands: PYR.24 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:R.70, E:R.70, C:S.120, C:A.121 Water bridges: E:A.174, C:N.129, C:N.129 SSN.30: 9 residues within 4Å: Chain B: V.118, G.119, S.120, A.121 Chain F: H.45, R.70, A.174, L.212 Ligands: PYR.29 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:R.70, F:R.70, B:S.120, B:A.121 Water bridges: F:A.174, B:N.129 Hydrophobic interactions: B:A.121

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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