SMTL ID : 2v5k.1

Class II aldolase HpcH - magnesium - oxamate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: Q.172, E.174, D.200 Ligands: OXM.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.174, A:D.200, H2O.2, H2O.26 MG.4: 4 residues within 4Å: Chain B: Q.172, E.174, D.200 Ligands: OXM.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.174, B:D.200, H2O.7, H2O.21 MG.7: 4 residues within 4Å: Chain C: Q.172, E.174, D.200 Ligands: OXM.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.174, C:D.200, H2O.4, H2O.13 MG.10: 4 residues within 4Å: Chain D: Q.172, E.174, D.200 Ligands: OXM.11 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.174, D:D.200, H2O.18, H2O.32 MG.13: 4 residues within 4Å: Chain E: Q.172, E.174, D.200 Ligands: OXM.14 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.174, E:D.200, H2O.15, H2O.24 MG.16: 4 residues within 4Å: Chain F: Q.172, E.174, D.200 Ligands: OXM.17 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.174, F:D.200, H2O.9, H2O.29

6 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 10 residues within 4Å: Chain A: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.95, A:Q.172, A:E.174, A:A.199, A:D.200 Water bridges: A:R.95, A:R.95, A:R.95 OXM.5: 10 residues within 4Å: Chain B: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.95, B:Q.172, B:A.199, B:D.200, B:D.200 Water bridges: B:R.95, B:R.95, B:R.95 OXM.8: 10 residues within 4Å: Chain C: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.95, C:Q.172, C:A.199, C:D.200 Water bridges: C:R.95, C:R.95, C:R.95 OXM.11: 10 residues within 4Å: Chain D: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.10 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.95, D:Q.172, D:A.199, D:D.200 Water bridges: D:R.95, D:R.95, D:R.95 OXM.14: 10 residues within 4Å: Chain E: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:R.95, E:Q.172, E:E.174, E:A.199, E:D.200 Water bridges: E:R.95, E:R.95, E:R.95 OXM.17: 10 residues within 4Å: Chain F: R.95, Q.172, E.174, F.195, G.197, P.198, A.199, D.200, L.237 Ligands: MG.16 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:R.95, F:Q.172, F:E.174, F:A.199, F:D.200 Water bridges: F:R.95, F:R.95, F:R.95

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

PO4.3: 6 residues within 4Å: Chain A: K.31, K.35, R.134, E.189, G.190, D.192 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.190, A:D.192 Water bridges: A:R.134, A:R.134, A:R.134, A:E.189 Salt bridges: A:K.31, A:K.35, A:R.134 PO4.6: 6 residues within 4Å: Chain B: K.31, K.35, R.134, E.189, G.190, D.192 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.192 Water bridges: B:K.31, B:R.134, B:R.134, B:G.190 Salt bridges: B:K.31, B:K.35, B:R.134 PO4.9: 6 residues within 4Å: Chain C: K.31, K.35, R.134, E.189, G.190, D.192 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.190, C:D.192 Water bridges: C:R.134, C:R.134, C:R.134 Salt bridges: C:K.31, C:K.35, C:R.134 PO4.12: 6 residues within 4Å: Chain D: K.31, K.35, R.134, E.189, G.190, D.192 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.192 Water bridges: D:K.31, D:R.134, D:R.134, D:G.190 Salt bridges: D:K.31, D:K.35, D:R.134 PO4.15: 6 residues within 4Å: Chain E: K.31, K.35, R.134, E.189, G.190, D.192 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.190, E:D.192 Water bridges: E:R.134, E:R.134, E:R.134, E:E.189 Salt bridges: E:K.31, E:K.35, E:R.134 PO4.18: 6 residues within 4Å: Chain F: K.31, K.35, R.134, E.189, G.190, D.192 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:E.189, F:D.192 Water bridges: F:K.31, F:R.134, F:R.134, F:G.190 Salt bridges: F:K.31, F:K.35, F:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rea, D. et al., Structure and Mechanism of Hpch: A Metal Ion Dependent Class II Aldolase from the Homoprotocatechuate Degradation Pathway of Escherichia Coli. J.Mol.Biol. (2007)

Release Date

2007-10-02

Peptides

2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE

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