SMTL ID : 2yc3.1

Inhibitors of the herbicidal target IspD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x MW5: 6-benzyl-5-chloro[1,2,4]triazolo[1,5-a]pyrimidin-7(3H)-one(Non-covalent)

MW5.1: 16 residues within 4Å: Chain A: R.83, I.103, A.129, V.130, Q.164, V.165, I.166, L.171, V.185, D.187, D.188, V.189, S.190, I.191, V.192, V.199 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.130, A:Q.164, A:I.166, A:L.171, A:V.189, A:V.192, A:V.192, A:V.199 Hydrogen bonds: A:R.83, A:Q.164, A:S.190, A:I.191, A:V.192 Water bridges: A:Q.84, A:D.188 MW5.9: 16 residues within 4Å: Chain B: R.83, I.103, A.129, V.130, Q.164, V.165, I.166, L.171, V.185, D.187, D.188, V.189, S.190, I.191, V.192, V.199 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.130, B:Q.164, B:I.166, B:L.171, B:V.189, B:V.192, B:V.192, B:V.199 Hydrogen bonds: B:R.83, B:Q.164, B:S.190, B:I.191, B:V.192 Water bridges: B:Q.84

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: E.65 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.65 NA.5: 2 residues within 4Å: Chain A: E.65 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.65 NA.10: 2 residues within 4Å: Chain B: E.65 Ligands: NA.13 No protein-ligand interaction detected (PLIP) NA.13: 2 residues within 4Å: Chain B: E.65 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.65

4 x CU: COPPER (II) ION(Non-covalent)

CU.3: 2 residues within 4Å: Chain A: T.212, D.216 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.216, A:D.216 CU.4: 2 residues within 4Å: Chain A: E.64, E.67 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.64, A:E.64, A:E.67, A:E.67, H2O.2 CU.11: 2 residues within 4Å: Chain B: T.212, D.216 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.216, B:D.216 CU.12: 2 residues within 4Å: Chain B: E.64, E.67 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.64, B:E.64, B:E.67, B:E.67, H2O.8

6 x CD: CADMIUM ION(Non-covalent)

CD.6: 3 residues within 4Å: Chain A: D.187, E.193 Chain B: K.140 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.187, A:E.193 CD.7: 2 residues within 4Å: Chain A: E.47, E.117 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.47, A:E.47, A:E.117, A:E.117 CD.8: 1 residues within 4Å: Chain A: E.93 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.93, A:E.93, H2O.3, H2O.3 CD.14: 3 residues within 4Å: Chain A: K.140 Chain B: D.187, E.193 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.187, B:E.193 CD.15: 2 residues within 4Å: Chain B: E.47, E.117 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.47, B:E.47, B:E.117, B:E.117 CD.16: 1 residues within 4Å: Chain B: E.93 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.93, B:E.93, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Witschel, M.C. et al., Inhibitors of the Herbicidal Target Ispd: Allosteric Site Binding. Angew.Chem.Int.Ed.Engl. (2011)

Release Date

2011-08-24

Peptides

2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC

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