SMTL ID : 1ofa.1

Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with phosphoenolpyruvate and cobalt(ii)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 6 residues within 4Å: Chain B: C.76, H.282, E.316, D.342 Ligands: PEP.5, GOL.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:H.282, B:E.316, B:D.342, H2O.6 CO.4: 5 residues within 4Å: Chain A: C.76, H.282, E.316, D.342 Ligands: PEP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.76, A:H.282, A:E.316, A:D.342, H2O.11

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 residues within 4Å: Chain A: R.107, Y.109, K.112, P.113, E.158, G.178, A.179, R.180, K.201, R.249, H.282, E.316 Ligands: CO.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.113 Hydrogen bonds: A:A.179 Water bridges: A:Y.109, A:K.112, A:E.158, A:R.180, A:R.180, A:R.180, A:K.201 Salt bridges: A:R.107, A:K.112, A:R.180, A:K.201, A:K.201, A:R.249, A:H.282, A:H.282 PEP.5: 13 residues within 4Å: Chain B: R.107, Y.109, K.112, P.113, E.158, G.178, A.179, R.180, K.201, R.249, H.282 Ligands: CO.1, GOL.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.113 Hydrogen bonds: B:A.179 Water bridges: B:R.107, B:K.112, B:R.180, B:R.180, B:R.249 Salt bridges: B:R.107, B:K.112, B:R.180, B:K.201, B:K.201, B:R.249, B:H.282, B:H.282

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.111, K.120, D.161 Chain B: Q.185, L.186, E.189, F.224 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.120, A:D.161, B:Q.185, B:E.189 Water bridges: A:N.124 GOL.6: 8 residues within 4Å: Chain A: Q.185, L.186, E.189, F.224 Chain B: E.111, K.120, L.160, D.161 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.120, B:D.161, A:E.189 Water bridges: B:N.124, A:E.189, A:M.225 GOL.7: 6 residues within 4Å: Chain B: K.112, P.113, T.341, D.342 Ligands: CO.1, PEP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.113 Water bridges: B:K.112, B:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koenig, V. et al., Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism. J.Mol.Biol. (2004)

Release Date

2004-04-08

Peptides

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

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