SMTL ID : 2ycm.1

Inhibitors of herbicidal target IspD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: K.48, D.94 Chain B: E.63, E.66 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.94, A:D.94, B:E.63, B:E.66, H2O.5 CD.2: 1 residues within 4Å: Chain A: H.196 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.196, H2O.4 CD.3: 3 residues within 4Å: Chain A: E.92 Chain B: E.92 Ligands: CD.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.92, B:E.92, A:E.92, A:E.92 CD.7: 4 residues within 4Å: Chain A: E.63, E.66 Chain B: K.48, D.94 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.63, A:E.66, B:D.94, B:D.94, H2O.1 CD.8: 1 residues within 4Å: Chain B: H.196 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.196, H2O.7 CD.9: 3 residues within 4Å: Chain A: E.92 Chain B: E.92 Ligands: CD.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.92, B:E.92, A:E.92, A:E.92

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

NA.4: 1 residues within 4Å: Chain A: E.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 NA.10: 1 residues within 4Å: Chain B: E.64 No protein-ligand interaction detected (PLIP)

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

CU.5: 1 residues within 4Å: Chain A: D.215 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.215, A:D.215 CU.11: 1 residues within 4Å: Chain B: D.215 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.215, B:D.215

2 x 30A: 6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXYLIC ACID(Non-covalent)

30A.6: 16 residues within 4Å: Chain A: R.82, Q.83, I.102, A.128, V.129, Q.163, V.164, I.165, V.184, D.186, D.187, V.188, S.189, I.190, V.191, V.198 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.129, A:Q.163, A:I.165, A:V.184, A:V.188, A:V.188, A:V.191, A:V.191, A:V.198 Hydrogen bonds: A:R.82, A:D.187, A:V.188, A:S.189, A:I.190, A:V.191 Salt bridges: A:R.82 30A.12: 16 residues within 4Å: Chain B: R.82, Q.83, I.102, A.128, V.129, Q.163, V.164, I.165, V.184, D.186, D.187, V.188, S.189, I.190, V.191, V.198 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.129, B:Q.163, B:I.165, B:V.184, B:V.188, B:V.188, B:V.191, B:V.191, B:V.198 Hydrogen bonds: B:R.82, B:V.188, B:S.189, B:I.190, B:V.191 Salt bridges: B:R.82

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