SMTL ID : 5mro.1

Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x Q9P: Azolopyrimidine(Non-covalent)

Q9P.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 14 PLIP interactions: 14 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:D.188 Q9P.8: 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 13 PLIP interactions: 13 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

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

TRS.2: 2 residues within 4Å: Chain A: L.218, E.221 No protein-ligand interaction detected (PLIP) TRS.9: 2 residues within 4Å: Chain B: L.218, E.221 No protein-ligand interaction detected (PLIP)

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.10: 4 residues within 4Å: Chain B: P.46, E.47, E.117 Ligands: CD.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.46

2 x K: POTASSIUM ION(Non-covalent)

K.4: 1 residues within 4Å: Chain A: D.216 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain B: D.216 No protein-ligand interaction detected (PLIP)

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.4, H2O.5 CD.6: 1 residues within 4Å: Chain A: D.95 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, H2O.3 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.12: 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.10 CD.13: 1 residues within 4Å: Chain B: D.95 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, H2O.9 CD.14: 3 residues within 4Å: Chain B: E.47, E.117 Ligands: ACT.10 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.10

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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