SMTL ID : 1vs1.1

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.46, H.216, E.242, D.253 Ligands: PEP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.46, A:H.216, A:E.242, A:D.253, H2O.1 MN.3: 5 residues within 4Å: Chain B: C.46, H.216, E.242, D.253 Ligands: PEP.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.46, B:H.216, B:E.242, B:D.253, H2O.2 MN.5: 5 residues within 4Å: Chain C: C.46, H.216, E.242, D.253 Ligands: PEP.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.46, C:H.216, C:E.242, C:D.253, H2O.5 MN.7: 5 residues within 4Å: Chain D: C.46, H.216, E.242, D.253 Ligands: PEP.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.46, D:H.216, D:E.242, D:D.253, H2O.6

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 residues within 4Å: Chain A: R.70, K.75, P.76, E.108, Q.126, G.128, A.129, R.130, K.151, R.181, H.216, E.242 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.76 Hydrogen bonds: A:Q.126, A:A.129 Water bridges: A:K.75, A:K.75, A:R.130, A:R.130 Salt bridges: A:R.70, A:K.75, A:R.130, A:K.151, A:K.151, A:R.181, A:H.216, A:H.216 PEP.4: 13 residues within 4Å: Chain B: R.70, K.75, P.76, E.108, Q.126, G.128, A.129, R.130, K.151, R.181, H.216, E.242 Ligands: MN.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.76 Hydrogen bonds: B:Q.126, B:A.129 Water bridges: B:E.108, B:R.130, B:R.130, B:R.181 Salt bridges: B:R.70, B:K.75, B:R.130, B:K.151, B:K.151, B:R.181, B:H.216, B:H.216 PEP.6: 13 residues within 4Å: Chain C: R.70, K.75, P.76, E.108, Q.126, G.128, A.129, R.130, K.151, R.181, H.216, E.242 Ligands: MN.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:P.76 Hydrogen bonds: C:Q.126, C:Q.126, C:A.129 Water bridges: C:K.75 Salt bridges: C:R.70, C:K.75, C:R.130, C:K.151, C:K.151, C:R.181, C:H.216, C:H.216 PEP.8: 13 residues within 4Å: Chain D: R.70, K.75, P.76, E.108, Q.126, G.128, A.129, R.130, K.151, R.181, H.216, E.242 Ligands: MN.7 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:P.76 Hydrogen bonds: D:Q.126, D:A.129 Water bridges: D:K.75, D:R.130, D:R.130, D:R.181 Salt bridges: D:R.70, D:K.75, D:R.130, D:K.151, D:K.151, D:R.181, D:H.216, D:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shumilin, I.A. et al., Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP. TO BE PUBLISHED

Release Date

2006-05-16

Peptides

3-deoxy-7-phosphoheptulonate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-deoxy-7-phosphoheptulonate synthase