SMTL ID : 4b5v.1

Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with 4-hydroxyl-2-ketoheptane-1,7-dioate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-hexamer

Ligands

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 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: E8U.2, MG.4 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, A:D.175 Water bridges: A:R.70 PYR.6: 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: E8U.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.170, B:L.212 Hydrogen bonds: B:R.70, B:Q.147, B:E.149, B:E.149, B:A.174, B:D.175 Water bridges: B:R.70, B:D.175 PYR.9: 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: E8U.10, MG.12 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, C:D.175 Water bridges: C:R.70 PYR.14: 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: E8U.15, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.170, D:L.212 Hydrogen bonds: D:R.70, D:Q.147, D:E.149, D:A.174, D:D.175 Water bridges: D:R.70, D:D.175 PYR.17: 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: E8U.18, MG.20 9 PLIP interactions: 9 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, E:D.175, E:D.175 Water bridges: E:R.70 PYR.22: 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: E8U.23, MG.24 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.170, F:L.212 Hydrogen bonds: F:R.70, F:Q.147, F:E.149, F:E.149, F:A.174, F:D.175 Water bridges: F:R.70

6 x E8U: (4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid(Non-covalent)

E8U.2: 19 residues within 4Å: Chain A: W.19, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Chain E: V.118, G.119, S.120, A.121, L.122 Ligands: PYR.1, MG.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:R.70, A:R.70, A:Q.147, A:A.174, A:D.175, E:S.120 Hydrophobic interactions: E:A.121 Water bridges: E:A.121, E:A.121 E8U.7: 20 residues within 4Å: Chain B: W.19, D.42, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Chain D: V.118, G.119, S.120, A.121, L.122 Ligands: PYR.6, MG.8 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:A.121, B:R.70, B:R.70, B:Q.147, B:A.174, B:D.175 Water bridges: B:D.175 E8U.10: 19 residues within 4Å: Chain A: V.118, G.119, S.120, A.121, L.122 Chain C: W.19, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Ligands: PYR.9, MG.12 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.70, C:R.70, C:Q.147, C:A.174, C:D.175, A:S.120 Hydrophobic interactions: A:A.121 Water bridges: A:A.121, A:A.121 E8U.15: 20 residues within 4Å: Chain D: W.19, D.42, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Chain F: V.118, G.119, S.120, A.121, L.122 Ligands: PYR.14, MG.16 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.70, D:R.70, D:Q.147, D:A.174, D:D.175, F:A.121 Water bridges: D:D.175 E8U.18: 19 residues within 4Å: Chain C: V.118, G.119, S.120, A.121, L.122 Chain E: W.19, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Ligands: PYR.17, MG.20 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:A.121 Hydrogen bonds: C:S.120, E:R.70, E:R.70, E:Q.147, E:A.174, E:D.175, E:D.175 Water bridges: C:A.121, C:A.121 E8U.23: 20 residues within 4Å: Chain B: V.118, G.119, S.120, A.121, L.122 Chain F: W.19, D.42, H.45, R.70, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212, V.234 Ligands: PYR.22, MG.24 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:A.121, F:R.70, F:R.70, F:Q.147, F:A.174, F:D.175

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: S.24, S.25, Y.26 Chain B: L.22, S.23, S.24, P.47 Chain D: L.54, T.55 Ligands: GOL.5 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:S.23, B:P.47, A:S.25, A:S.25, A:S.27 Hydrogen bonds: A:S.24 GOL.5: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.24 Water bridges: B:S.25, B:S.25, B:S.25, B:S.25, B:S.27 GOL.11: 10 residues within 4Å: Chain C: S.24, S.25, Y.26 Chain D: L.22, S.23, S.24, P.47 Chain F: L.54, T.55 Ligands: GOL.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.24 Water bridges: C:S.25, C:S.25, C:S.27, D:S.23, D:P.47 GOL.13: 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 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.24 Water bridges: D:S.25, D:S.25, D:S.25, D:S.25, D:S.27 GOL.19: 10 residues within 4Å: Chain B: 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 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.24 Water bridges: E:S.25, E:S.25, E:S.27, F:S.23, F:P.47 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.19 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.24 Water bridges: F:S.25, F:S.25, F:S.25, F:S.25, F:S.27

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: PYR.1, E8U.2 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.8: 7 residues within 4Å: Chain B: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.6, E8U.7 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.12: 7 residues within 4Å: Chain C: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.9, E8U.10 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: PYR.14, E8U.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, H2O.52, H2O.52 MG.20: 7 residues within 4Å: Chain E: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.17, E8U.18 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, H2O.67, H2O.67 MG.24: 7 residues within 4Å: Chain F: R.70, Q.147, E.149, G.172, D.175 Ligands: PYR.22, E8U.23 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.82, H2O.83

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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