SMTL ID : 5mrm.1

Arabidopsis thaliana IspD in complex with Isoxazole (4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x Q9T: 2,4-bis(bromanyl)-6-[3-(trifluoromethyl)-1,2-oxazol-5-yl]phenol(Non-covalent)

Q9T.1: 15 residues within 4Å: Chain A: R.83, Q.84, V.87, I.103, A.129, Q.164, V.165, I.166, L.171, F.175, S.190, I.191, V.192, E.193, V.199 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.164, A:V.192, A:V.192, A:V.199 Hydrogen bonds: A:Q.164, A:S.190 Water bridges: A:S.190 pi-Cation interactions: A:R.83 Halogen bonds: A:V.165, A:E.193 Q9T.9: 15 residues within 4Å: Chain B: R.83, Q.84, V.87, I.103, A.129, Q.164, V.165, I.166, L.171, F.175, S.190, I.191, V.192, E.193, V.199 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.164, B:V.192, B:V.192, B:V.199 Hydrogen bonds: B:Q.164, B:S.190 Water bridges: B:S.190 pi-Cation interactions: B:R.83 Halogen bonds: B:V.165, B:E.193

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: K.121, D.122, A.125, V.126, Y.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121, A:Y.200 TRS.10: 5 residues within 4Å: Chain B: K.121, D.122, A.125, V.126, Y.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.121, B:D.122, B:Y.200

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

ACT.3: 4 residues within 4Å: Chain A: P.46, E.47, E.117 Ligands: CD.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.46 ACT.11: 4 residues within 4Å: Chain B: P.46, E.47, E.117 Ligands: CD.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.46

4 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: E.67, L.74 No protein-ligand interaction detected (PLIP) K.5: 1 residues within 4Å: Chain A: D.95 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:D.95, H2O.3 K.12: 2 residues within 4Å: Chain B: E.67, L.74 No protein-ligand interaction detected (PLIP) K.13: 1 residues within 4Å: Chain B: D.95 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, B:D.95, H2O.8

6 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.6: 2 residues within 4Å: Chain A: E.64, E.67 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.64, A:E.67, A:E.67, H2O.2 CD.7: 3 residues within 4Å: Chain A: E.47, E.117 Ligands: ACT.3 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.3 CD.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CD.14: 2 residues within 4Å: Chain B: E.64, E.67 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.64, B:E.67, B:E.67, H2O.7 CD.15: 3 residues within 4Å: Chain B: E.47, E.117 Ligands: ACT.11 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.11 CD.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwab, A. et al., Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands. ACS Chem. Biol. (2017)

Release Date

2017-07-19

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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