SMTL ID : 1kfl.1 (1 other biounit)

Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from E.coli complexed with Mn2+, PEP, and Phe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: C.61, R.92, K.97, H.268, E.302, D.326 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, R.92, H.268, E.302, D.326 Ligands: PEP.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:H.268, B:E.302, B:D.326 MN.11: 6 residues within 4Å: Chain C: C.61, R.92, K.97, H.268, E.302, D.326 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.61, C:H.268, C:E.302, C:D.326 MN.16: 5 residues within 4Å: Chain D: C.61, R.92, H.268, E.302, D.326 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.61, D:H.268, D:E.302, D:D.326

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

SO4.2: 5 residues within 4Å: Chain A: R.9 Chain B: G.225, N.226, G.227, D.228 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.227, B:D.228 Salt bridges: A:R.9 SO4.3: 3 residues within 4Å: Chain A: T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.193, A:K.194 SO4.7: 4 residues within 4Å: Chain A: G.225, G.227, D.228 Chain B: R.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.9 Hydrogen bonds: A:G.227, A:D.228 SO4.8: 3 residues within 4Å: Chain B: T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.193, B:K.194 SO4.12: 4 residues within 4Å: Chain C: R.9 Chain D: G.225, G.227, D.228 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.227, D:D.228 Salt bridges: C:R.9 SO4.13: 3 residues within 4Å: Chain C: T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.193, C:K.194 SO4.17: 5 residues within 4Å: Chain C: G.225, N.226, G.227, D.228 Chain D: R.9 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.9 Hydrogen bonds: C:G.227, C:D.228 SO4.18: 3 residues within 4Å: Chain D: T.192, I.193, K.194 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.193, D:K.194

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.4: 14 residues within 4Å: Chain A: M.147, P.150, Q.151, A.154, G.178, L.179, S.180, F.209, S.211, K.214, V.221 Chain B: D.6, D.7, I.10 13 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.10, A:P.150, A:Q.151, A:F.209, A:F.209, A:V.221 Hydrogen bonds: B:D.6, B:D.6, B:D.7, A:Q.151, A:S.180, A:K.214, F.4 PHE.9: 14 residues within 4Å: Chain A: D.6, D.7, I.10 Chain B: M.147, P.150, Q.151, A.154, G.178, L.179, S.180, F.209, S.211, K.214, V.221 14 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.150, B:Q.151, B:F.209, B:F.209, B:V.221, A:I.10 Hydrogen bonds: B:Q.151, B:S.180, B:K.214, A:D.6, A:D.6, A:D.7, A:D.7, F.9 PHE.14: 14 residues within 4Å: Chain C: M.147, P.150, Q.151, A.154, G.178, L.179, S.180, F.209, S.211, K.214, V.221 Chain D: D.6, D.7, I.10 12 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 8 interactions with chain C Hydrophobic interactions: D:I.10, C:P.150, C:Q.151, C:F.209, C:F.209, C:V.221 Hydrogen bonds: D:D.6, D:D.7, F.14, C:Q.151, C:S.180, C:K.214 PHE.19: 14 residues within 4Å: Chain C: D.6, D.7, I.10 Chain D: M.147, P.150, Q.151, A.154, G.178, L.179, S.180, F.209, S.211, K.214, V.221 11 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.10, D:P.150, D:Q.151, D:F.209, D:V.221 Hydrogen bonds: C:D.6, C:D.7, D:Q.151, D:S.180, D:K.214, F.19

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.5: 7 residues within 4Å: Chain A: R.92, Y.94, E.143, K.186, R.234, H.268, M.300 6 PLIP interactions: 6 interactions with chain A Salt bridges: A:R.92, A:K.186, A:K.186, A:R.234, A:H.268, A:H.268 PEP.10: 8 residues within 4Å: Chain B: R.92, Y.94, E.143, K.186, R.234, H.268, M.300 Ligands: MN.6 6 PLIP interactions: 6 interactions with chain B Salt bridges: B:R.92, B:K.186, B:K.186, B:R.234, B:H.268, B:H.268 PEP.15: 8 residues within 4Å: Chain C: R.92, Y.94, E.143, A.164, K.186, R.234, H.268, M.300 6 PLIP interactions: 6 interactions with chain C Salt bridges: C:R.92, C:K.186, C:K.186, C:R.234, C:H.268, C:H.268 PEP.20: 7 residues within 4Å: Chain D: R.92, Y.94, E.143, K.186, R.234, H.268, M.300 6 PLIP interactions: 6 interactions with chain D Salt bridges: D:R.92, D:K.186, D:K.186, D:R.234, D:H.268, D:H.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shumilin, I.A. et al., Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates. J.Mol.Biol. (2002)

Release Date

2002-08-23

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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