SMTL ID : 2yc5.1

Inhibitors of the herbicidal target IspD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 6BC: 5-chloro-7-hydroxy-6-(phenylmethyl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

6BC.1: 17 residues within 4Å: Chain A: R.83, Q.84, 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 12 PLIP interactions: 12 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:I.191, A:V.192 6BC.13: 17 residues within 4Å: Chain B: R.83, Q.84, 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 12 PLIP interactions: 12 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:I.191, B:V.192

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

CU.2: 3 residues within 4Å: Chain A: E.67, D.73, L.74 No protein-ligand interaction detected (PLIP) CU.3: 2 residues within 4Å: Chain A: K.49, D.73 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.73, H2O.2, H2O.3 CU.6: 1 residues within 4Å: Chain A: D.216 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.216, H2O.7 CU.14: 3 residues within 4Å: Chain B: E.67, D.73, L.74 No protein-ligand interaction detected (PLIP) CU.15: 2 residues within 4Å: Chain B: K.49, D.73 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.73, H2O.9, H2O.9 CU.18: 1 residues within 4Å: Chain B: D.216 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.216, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: H.197 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.197 MG.16: 1 residues within 4Å: Chain B: H.197 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.197

6 x CD: CADMIUM ION(Non-covalent)

CD.5: 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.9: 3 residues within 4Å: Chain A: D.187, E.193 Chain B: K.140 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:D.187, A:E.193, H2O.11 CD.12: 2 residues within 4Å: Chain A: D.95, N.97 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.95, A:D.95 CD.17: 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.9, H2O.9 CD.21: 3 residues within 4Å: Chain A: K.140 Chain B: D.187, E.193 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.187, B:E.193, H2O.5 CD.24: 2 residues within 4Å: Chain B: D.95, N.97 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.95, B:D.95

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain A: L.218, E.221 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.218 ACT.8: 4 residues within 4Å: Chain A: P.46, E.47, E.117 Ligands: ZN.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.46 ACT.19: 2 residues within 4Å: Chain B: L.218, E.221 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.218 ACT.20: 4 residues within 4Å: Chain B: P.46, E.47, E.117 Ligands: ZN.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.46

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

NA.10: 1 residues within 4Å: Chain A: D.61 No protein-ligand interaction detected (PLIP) NA.22: 1 residues within 4Å: Chain B: D.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.61

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: E.47, E.117 Ligands: ACT.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.47, A:E.47, A:E.117, A:E.117, ACT.8 ZN.23: 3 residues within 4Å: Chain B: E.47, E.117 Ligands: ACT.20 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.47, B:E.47, B:E.117, B:E.117, ACT.20

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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