SMTL ID : 2v5j.1

Apo Class II aldolase HpcH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: K.31, K.35, R.134, E.189, G.190, D.192 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:K.31, A:R.134, A:G.190, A:G.190 Salt bridges: A:K.31, A:K.35, A:R.134 PO4.5: 6 residues within 4Å: Chain B: K.31, K.35, R.134, E.189, G.190, D.192 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.189, B:D.192 Water bridges: B:K.31, B:K.31, B:K.35, B:R.134, B:R.134, B:D.165, B:G.190, B:G.190 Salt bridges: B:K.31, B:K.35, B:R.134 PO4.8: 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:D.192 Water bridges: C:K.31, C:R.134, C:G.190, C:G.190 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:E.189, D:D.192 Water bridges: D:K.31, D:K.31, D:K.35, D:R.134, D:R.134, D:D.165, D:G.190, 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 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.192 Water bridges: E:K.31, E:R.134, E:G.190, E:G.190 Salt bridges: E:K.31, E:K.35, E:R.134 PO4.19: 6 residues within 4Å: Chain F: K.31, K.35, R.134, E.189, G.190, D.192 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:E.189, F:D.192 Water bridges: F:K.31, F:K.31, F:K.35, F:R.134, F:R.134, F:D.165, F:G.190, F:G.190 Salt bridges: F:K.31, F:K.35, F:R.134

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: S.49, S.50, Y.51 Chain B: L.47, S.48, S.49 Chain F: Q.76, L.79, T.80 Ligands: GOL.6 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: A:S.50, A:S.50, A:Y.51, B:S.48 Water bridges: A:S.52, F:Q.76 GOL.3: 6 residues within 4Å: Chain A: A.25, G.111, Q.113, A.150, R.152, Y.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.152, A:R.152 Water bridges: A:Q.113, A:R.149 GOL.4: 8 residues within 4Å: Chain A: L.34, K.35, G.37, R.228, G.231, K.232, A.233, L.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.228, A:G.231 Water bridges: A:K.35, A:A.36, A:A.233 GOL.6: 9 residues within 4Å: Chain A: L.47, S.48, S.49 Chain B: S.49, S.50, Y.51 Chain C: Q.76, L.79 Ligands: GOL.2 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:S.50, B:S.50, B:Y.51, A:S.48 Water bridges: B:S.52, C:Q.76 GOL.7: 6 residues within 4Å: Chain B: A.25, G.111, Q.113, A.150, R.152, Y.159 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.111, B:R.152, B:R.152 Water bridges: B:A.25, B:Q.113, B:Q.113, B:R.149 GOL.9: 10 residues within 4Å: Chain B: Q.76, L.79, T.80 Chain C: S.49, S.50, Y.51 Chain D: L.47, S.48, S.49 Ligands: GOL.13 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:S.50, C:S.50, C:Y.51, D:S.48 Water bridges: C:S.52, B:Q.76 GOL.10: 6 residues within 4Å: Chain C: A.25, G.111, Q.113, A.150, R.152, Y.159 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.152, C:R.152 Water bridges: C:Q.113, C:R.149 GOL.11: 8 residues within 4Å: Chain C: L.34, K.35, G.37, R.228, G.231, K.232, A.233, L.253 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.228, C:G.231 Water bridges: C:K.35, C:A.36, C:A.233 GOL.13: 9 residues within 4Å: Chain C: L.47, S.48, S.49 Chain D: S.49, S.50, Y.51 Chain E: Q.76, L.79 Ligands: GOL.9 6 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D, 1 interactions with chain C Water bridges: E:Q.76, D:S.52 Hydrogen bonds: D:S.50, D:S.50, D:Y.51, C:S.48 GOL.14: 6 residues within 4Å: Chain D: A.25, G.111, Q.113, A.150, R.152, Y.159 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.111, D:R.152, D:R.152 Water bridges: D:A.25, D:Q.113, D:Q.113, D:R.149 GOL.16: 10 residues within 4Å: Chain D: Q.76, L.79, T.80 Chain E: S.49, S.50, Y.51 Chain F: L.47, S.48, S.49 Ligands: GOL.20 6 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E, 1 interactions with chain F Water bridges: D:Q.76, E:S.52 Hydrogen bonds: E:S.50, E:S.50, E:Y.51, F:S.48 GOL.17: 6 residues within 4Å: Chain E: A.25, G.111, Q.113, A.150, R.152, Y.159 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.152, E:R.152 Water bridges: E:Q.113, E:R.149 GOL.18: 8 residues within 4Å: Chain E: L.34, K.35, G.37, R.228, G.231, K.232, A.233, L.253 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.228, E:G.231 Water bridges: E:K.35, E:A.36, E:A.233 GOL.20: 9 residues within 4Å: Chain A: Q.76, L.79 Chain E: L.47, S.48, S.49 Chain F: S.49, S.50, Y.51 Ligands: GOL.16 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 4 interactions with chain F Hydrogen bonds: E:S.48, F:S.50, F:S.50, F:Y.51 Water bridges: A:Q.76, F:S.52 GOL.21: 6 residues within 4Å: Chain F: A.25, G.111, Q.113, A.150, R.152, Y.159 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.111, F:R.152, F:R.152 Water bridges: F:A.25, F:Q.113, F:Q.113, F:R.149

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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