SMTL ID : 4nan.1

Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 2JM: 2-bromo-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol(Non-covalent)

2JM.1: 10 residues within 4Å: Chain A: V.87, A.129, V.130, Q.164, V.165, L.171, I.191, V.192, V.199 Ligands: CD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.164, A:V.199 Hydrogen bonds: A:Q.164 2JM.14: 10 residues within 4Å: Chain B: V.87, A.129, V.130, Q.164, V.165, L.171, I.191, V.192, V.199 Ligands: CD.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.164, B:V.199 Hydrogen bonds: B:Q.164

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

DTT.2: 3 residues within 4Å: Chain A: K.121, A.125 Ligands: K.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121, A:K.121 DTT.15: 3 residues within 4Å: Chain B: K.121, A.125 Ligands: K.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.121, B:K.121

8 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: Q.164 Ligands: 2JM.1, CL.13 No protein-ligand interaction detected (PLIP) 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: E.64, E.67 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.64, A:E.67, A:E.67 CD.6: 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: 3 residues within 4Å: Chain B: Q.164 Ligands: 2JM.14, CL.26 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: E.64, E.67 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.64, B:E.67, B:E.67 CD.19: 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.4

12 x K: POTASSIUM ION(Non-covalent)

K.7: 2 residues within 4Å: Chain A: T.212, D.216 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.216, A:D.216 K.8: 2 residues within 4Å: Chain A: A.125 Ligands: DTT.2 No protein-ligand interaction detected (PLIP) K.9: 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.10: 5 residues within 4Å: Chain A: I.34, A.35, S.38, S.106, P.109 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.34, A:S.38, A:S.106 K.11: 5 residues within 4Å: Chain A: S.43, M.45, V.48, D.71, V.72 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.43, A:M.45 K.12: 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.20: 2 residues within 4Å: Chain B: T.212, D.216 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.216, B:D.216 K.21: 2 residues within 4Å: Chain B: A.125 Ligands: DTT.15 No protein-ligand interaction detected (PLIP) K.22: 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.23: 5 residues within 4Å: Chain B: I.34, A.35, S.38, S.106, P.109 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.34, B:S.38, B:S.106 K.24: 5 residues within 4Å: Chain B: S.43, M.45, V.48, D.71, V.72 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.43, B:M.45 K.25: 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.4, H2O.4

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Chain A: D.187 Ligands: CD.3 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: D.187 Ligands: CD.16 Ligand excluded by PLIP

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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