SMTL ID : 5mrp.1

Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 15 residues within 4Å: Chain A: R.83, Q.84, I.103, A.129, Q.164, V.165, I.166, V.185, D.187, D.188, V.189, S.190, I.191, V.192, V.199 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.164, A:I.166, A:V.189, A:I.191, A:V.192, A:V.192, A:V.199 Hydrogen bonds: A:R.83, A:Q.164, A:D.188, A:S.190, A:I.191, A:V.192 6BC.7: 15 residues within 4Å: Chain B: R.83, Q.84, I.103, A.129, Q.164, V.165, I.166, 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:Q.164, B:I.166, B:V.189, B:I.191, 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

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.2: 1 residues within 4Å: Chain A: D.216 No protein-ligand interaction detected (PLIP) K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.8: 1 residues within 4Å: Chain B: D.216 No protein-ligand interaction detected (PLIP) K.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: K.49, D.95 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.95, A:D.95 CD.5: 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.6: 1 residues within 4Å: Chain A: E.93 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.93 CD.10: 2 residues within 4Å: Chain B: K.49, D.95 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.95, B:D.95 CD.11: 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.12: 1 residues within 4Å: Chain B: E.93 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.93

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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