SMTL ID : 4nak.1

Arabidopsis thaliana IspD in complex with pentabromo-pseudilin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x PBQ: PENTABROMOPSEUDILIN

PBQ.1: 13 residues within 4Å: Chain A: R.83, V.87, A.128, A.129, Q.164, V.165, L.171, F.175, S.190, I.191, V.192 Chain B: K.140 Ligands: CD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.164 Hydrogen bonds: A:S.190 Halogen bonds: A:V.165 PBQ.14: 13 residues within 4Å: Chain A: K.140 Chain B: R.83, V.87, A.128, A.129, Q.164, V.165, L.171, F.175, S.190, I.191, V.192 Ligands: CD.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.164 Hydrogen bonds: B:Q.164, B:S.190 Halogen bonds: B:V.165

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 2 residues within 4Å: Chain A: K.121 Ligands: K.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121, A:K.121 DTT.15: 2 residues within 4Å: Chain B: K.121 Ligands: K.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.121, B:K.121

10 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: Q.164 Ligands: PBQ.1 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: PBQ.1 CD.4: 1 residues within 4Å: Chain A: E.93 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.93, A:E.93 CD.5: 2 residues within 4Å: Chain A: R.83, D.187 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.187, A:D.187, H2O.1, H2O.3 CD.6: 2 residues within 4Å: Chain A: E.64, E.67 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.64, A:E.67, A:E.67 CD.7: 1 residues within 4Å: Chain A: H.197 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.197, H2O.1 CD.16: 2 residues within 4Å: Chain B: Q.164 Ligands: PBQ.14 No protein-ligand interaction detected (PLIP) CD.17: 1 residues within 4Å: Chain B: E.93 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.93, B:E.93 CD.18: 2 residues within 4Å: Chain B: R.83, D.187 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.187, B:D.187, H2O.4, H2O.5 CD.19: 2 residues within 4Å: Chain B: E.64, E.67 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.64, B:E.67, B:E.67 CD.20: 1 residues within 4Å: Chain B: H.197 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.197, H2O.3

12 x K: POTASSIUM ION(Non-covalent)

K.8: 1 residues within 4Å: Chain A: D.216 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.216 K.9: 2 residues within 4Å: Chain A: A.125 Ligands: DTT.2 No protein-ligand interaction detected (PLIP) K.10: 6 residues within 4Å: Chain A: R.108, P.109, L.110, V.111, N.208, I.209 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.209 K.11: 6 residues within 4Å: Chain A: I.34, A.35, S.38, S.106, R.108, P.109 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.34, A:S.38, A:S.106 K.12: 5 residues within 4Å: Chain A: S.43, M.45, V.48, D.71, V.72 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:M.45 K.13: 5 residues within 4Å: Chain A: V.111, N.112, D.115, S.205, N.208 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.115, H2O.1, H2O.1 K.21: 1 residues within 4Å: Chain B: D.216 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.216 K.22: 2 residues within 4Å: Chain B: A.125 Ligands: DTT.15 No protein-ligand interaction detected (PLIP) K.23: 6 residues within 4Å: Chain B: R.108, P.109, L.110, V.111, N.208, I.209 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.209 K.24: 6 residues within 4Å: Chain B: I.34, A.35, S.38, S.106, R.108, P.109 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.34, B:S.38, B:S.106 K.25: 5 residues within 4Å: Chain B: S.43, M.45, V.48, D.71, V.72 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:M.45 K.26: 5 residues within 4Å: Chain B: V.111, N.112, D.115, S.205, N.208 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.115, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunfermann, A. et al., Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme IspD. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-01-29

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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