SMTL ID : 4b5s.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-hexamer

Ligands

3 x 3GR: D-Glyceraldehyde(Non-covalent)

3GR.1: 10 residues within 4Å: Chain A: S.24, S.25, Y.26 Chain B: L.22, S.23, S.24, P.47 Chain F: Q.51, L.54, T.55 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.24, F:Q.51 3GR.13: 10 residues within 4Å: Chain B: Q.51, L.54, T.55 Chain C: S.24, S.25, Y.26 Chain D: L.22, S.23, S.24, P.47 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.51, C:S.24 3GR.25: 10 residues within 4Å: Chain D: Q.51, L.54, T.55 Chain E: S.24, S.25, Y.26 Chain F: L.22, S.23, S.24, P.47 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.24, D:Q.51

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

CO.2: 7 residues within 4Å: Chain A: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.5, MG.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, H2O.6, H2O.6 CO.8: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.11, MG.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, H2O.26, H2O.27 CO.14: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.17, MG.18 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, H2O.48, H2O.48 CO.20: 7 residues within 4Å: Chain D: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.23, MG.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, H2O.68, H2O.69 CO.26: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.29, MG.30 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, H2O.90, H2O.90 CO.32: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.35, MG.36 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.110, H2O.111

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

PO4.3: 7 residues within 4Å: Chain A: A.174 Chain C: V.118, G.119, S.120, A.121, N.129, L.135 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.120, C:S.120, C:A.121, C:N.129 Water bridges: A:A.174 PO4.4: 6 residues within 4Å: Chain A: L.9, K.10, A.11, G.12, R.203, L.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.9 Water bridges: A:R.203, A:R.203, A:R.203, A:R.203 Salt bridges: A:R.203 PO4.9: 7 residues within 4Å: Chain B: A.174 Chain F: V.118, G.119, S.120, A.121, L.122, N.129 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:S.120, F:A.121, F:N.129 Water bridges: F:V.118, F:S.120, B:A.174 PO4.10: 6 residues within 4Å: Chain B: L.9, K.10, G.12, R.203, G.206, L.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.10 Water bridges: B:K.10, B:A.11, B:R.203 Salt bridges: B:R.203 PO4.15: 7 residues within 4Å: Chain C: A.174 Chain E: V.118, G.119, S.120, A.121, N.129, L.135 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:S.120, E:S.120, E:A.121, E:N.129 Water bridges: C:A.174 PO4.16: 6 residues within 4Å: Chain C: L.9, K.10, A.11, G.12, R.203, L.228 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.9 Water bridges: C:R.203, C:R.203, C:R.203, C:R.203 Salt bridges: C:R.203 PO4.21: 7 residues within 4Å: Chain B: V.118, G.119, S.120, A.121, L.122, N.129 Chain D: A.174 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.120, B:A.121, B:N.129 Water bridges: B:V.118, B:S.120, D:A.174 PO4.22: 6 residues within 4Å: Chain D: L.9, K.10, G.12, R.203, G.206, L.228 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.10 Water bridges: D:K.10, D:A.11, D:R.203 Salt bridges: D:R.203 PO4.27: 7 residues within 4Å: Chain A: V.118, G.119, S.120, A.121, N.129, L.135 Chain E: A.174 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.120, A:S.120, A:A.121, A:N.129 Water bridges: E:A.174 PO4.28: 6 residues within 4Å: Chain E: L.9, K.10, A.11, G.12, R.203, L.228 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:L.9 Water bridges: E:R.203, E:R.203, E:R.203, E:R.203 Salt bridges: E:R.203 PO4.33: 7 residues within 4Å: Chain D: V.118, G.119, S.120, A.121, L.122, N.129 Chain F: A.174 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:S.120, D:A.121, D:N.129 Water bridges: D:V.118, D:S.120, F:A.174 PO4.34: 6 residues within 4Å: Chain F: L.9, K.10, G.12, R.203, G.206, L.228 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.10 Water bridges: F:K.10, F:A.11, F:R.203 Salt bridges: F:R.203

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.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.2, MG.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.170, A:L.212 Hydrogen bonds: A:R.70, A:Q.147, A:A.174, A:D.175 Water bridges: A:R.70, A:R.70 PYR.11: 11 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.8, MG.12 7 PLIP interactions: 7 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 PYR.17: 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.14, MG.18 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: 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 PYR.23: 11 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.20, MG.24 7 PLIP interactions: 7 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 PYR.29: 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.26, MG.30 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.170, E:L.212 Hydrogen bonds: E:R.70, E:Q.147, E:A.174, E:D.175 Water bridges: E:R.70, E:R.70 PYR.35: 11 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.32, MG.36 7 PLIP interactions: 7 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

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.2, PYR.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, H2O.6, H2O.6 MG.12: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.8, PYR.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, H2O.26, H2O.27 MG.18: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.14, PYR.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, H2O.48, H2O.48 MG.24: 7 residues within 4Å: Chain D: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.20, PYR.23 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, H2O.68, H2O.69 MG.30: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.26, PYR.29 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, H2O.90, H2O.90 MG.36: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: CO.32, PYR.35 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.110, H2O.111

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: L.22, S.23, S.24, P.47 Chain B: S.24, S.25, Y.26 Chain C: L.54, T.55 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.22 Water bridges: A:S.23, A:P.47, B:S.25, B:S.25, B:S.27 GOL.19: 9 residues within 4Å: Chain C: L.22, S.23, S.24, P.47 Chain D: S.24, S.25, Y.26 Chain E: L.54, T.55 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:L.22 Water bridges: C:S.23, C:P.47, D:S.25, D:S.25, D:S.27 GOL.31: 9 residues within 4Å: Chain A: L.54, T.55 Chain E: L.22, S.23, S.24, P.47 Chain F: S.24, S.25, Y.26 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E Water bridges: F:S.25, F:S.25, F:S.27, E:S.23, E:P.47 Hydrogen bonds: E:L.22

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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