SMTL ID : 1gg1.1

CRYSTAL STRUCTURE ANALYSIS OF DAHP SYNTHASE IN COMPLEX WITH MN2+ AND 2-PHOSPHOGLYCOLATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.1: 11 residues within 4Å: Chain A: R.92, Y.94, K.97, G.163, A.164, R.165, K.186, R.234, H.268, E.302 Ligands: MN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.164 Water bridges: A:R.92, A:R.165, A:R.165 Salt bridges: A:R.92, A:K.97, A:R.165, A:K.186, A:K.186, A:R.234, A:H.268, A:H.268 PGA.5: 11 residues within 4Å: Chain B: R.92, Y.94, K.97, G.163, A.164, R.165, K.186, R.234, H.268, E.302 Ligands: MN.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.164 Water bridges: B:R.92, B:K.97, B:E.143, B:R.165, B:R.165, B:R.165, B:R.234 Salt bridges: B:R.92, B:K.97, B:R.165, B:K.186, B:K.186, B:R.234, B:H.268, B:H.268 PGA.9: 13 residues within 4Å: Chain C: C.61, R.92, Y.94, K.97, G.163, A.164, R.165, K.186, R.234, H.268, E.302, D.326 Ligands: MN.10 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.164 Water bridges: C:R.92, C:K.97, C:R.165, C:R.165 Salt bridges: C:R.92, C:K.97, C:R.165, C:K.186, C:K.186, C:R.234, C:H.268, C:H.268 PGA.13: 11 residues within 4Å: Chain D: R.92, Y.94, K.97, G.163, A.164, R.165, K.186, R.234, H.268, E.302 Ligands: MN.14 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:A.164 Water bridges: D:Y.94, D:K.97, D:R.165, D:R.165, D:R.165, D:R.165 Salt bridges: D:R.92, D:K.97, D:R.165, D:K.186, D:K.186, D:R.234, D:H.268, D:H.268

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: C.61, K.97, H.268, E.302, D.326 Ligands: PGA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:H.268, A:E.302, A:D.326 MN.6: 6 residues within 4Å: Chain B: C.61, K.97, H.268, E.302, D.326 Ligands: PGA.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.61, B:H.268, B:E.302, B:D.326, H2O.6 MN.10: 6 residues within 4Å: Chain C: C.61, K.97, H.268, E.302, D.326 Ligands: PGA.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.61, C:H.268, C:E.302, C:D.326, H2O.18 MN.14: 6 residues within 4Å: Chain D: C.61, K.97, H.268, E.302, D.326 Ligands: PGA.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.61, D:H.268, D:E.302, D:D.326, H2O.22

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.99, T.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.100, A:T.100 Water bridges: A:D.326 Salt bridges: A:R.99 SO4.4: 4 residues within 4Å: Chain A: G.191, T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.193, A:K.194 SO4.7: 2 residues within 4Å: Chain B: R.99, T.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.100 Water bridges: B:R.99, B:T.101 Salt bridges: B:R.99 SO4.8: 4 residues within 4Å: Chain B: G.191, T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.193, B:K.194 SO4.11: 2 residues within 4Å: Chain C: R.99, T.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.100 Water bridges: C:D.326 Salt bridges: C:R.99 SO4.12: 4 residues within 4Å: Chain C: G.191, T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.193, C:K.194 SO4.15: 2 residues within 4Å: Chain D: R.99, T.100 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.100 Water bridges: D:T.100, D:V.102, D:K.273, D:D.326, D:D.326 Salt bridges: D:R.99 SO4.16: 4 residues within 4Å: Chain D: G.191, T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.193, D:K.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Structure of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli: comparison of the Mn(2+)*2-phosphoglycolate and the Pb(2+)*2-phosphoenolpyruvate complexes and implications for catalysis. J.Mol.Biol. (2000)

Release Date

2000-10-04

Peptides

3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE

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