SMTL ID : 4nal.1

Arabidopsis thaliana IspD in complex with tribromodichloro-pseudilin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x H70: 2,4-DICHLORO-6-(3,4,5-TRIBROMO-1H-PYRROL-2-YL)PHENOL(Non-covalent)

H70.1: 15 residues within 4Å: Chain A: R.83, V.87, A.128, A.129, V.130, Q.164, V.165, L.171, F.175, S.190, I.191, V.192, V.199 Chain B: K.140 Ligands: CD.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.130, A:Q.164, A:V.192, A:V.192, A:V.199 Hydrogen bonds: A:Q.164, A:S.190 Halogen bonds: A:V.165 H70.15: 15 residues within 4Å: Chain A: K.140 Chain B: R.83, V.87, A.128, A.129, V.130, Q.164, V.165, L.171, F.175, S.190, I.191, V.192, V.199 Ligands: CD.17 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.130, B:Q.164, B:V.192, B:V.192, B:V.199 Hydrogen bonds: B:Q.164, B:Q.164, B:S.190 Water bridges: B:S.190, A:K.140 Halogen bonds: B:V.165

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

DTT.2: 5 residues within 4Å: Chain A: D.122, A.125, V.126, Y.200 Ligands: K.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.200 DTT.16: 5 residues within 4Å: Chain B: D.122, A.125, V.126, Y.200 Ligands: K.23 No protein-ligand interaction detected (PLIP)

10 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: Q.164 Ligands: H70.1 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: H70.1, H2O.2 CD.4: 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.1, H2O.2 CD.5: 1 residues within 4Å: Chain A: D.187 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.1, H2O.1, H2O.2, H2O.5 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.17: 2 residues within 4Å: Chain B: Q.164 Ligands: H70.15 No protein-ligand interaction detected (PLIP) CD.18: 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.3, H2O.5 CD.19: 1 residues within 4Å: Chain B: D.187 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.2, H2O.3, H2O.3, H2O.3, H2O.5 CD.20: 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.21: 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

14 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: 7 residues within 4Å: Chain A: R.108, P.109, L.110, V.111, T.207, 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: 6 residues within 4Å: Chain A: K.3, 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.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.14: 1 residues within 4Å: Chain A: D.73 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.73, H2O.1 K.22: 1 residues within 4Å: Chain B: D.216 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.216 K.23: 2 residues within 4Å: Chain B: A.125 Ligands: DTT.16 No protein-ligand interaction detected (PLIP) K.24: 7 residues within 4Å: Chain B: R.108, P.109, L.110, V.111, T.207, N.208, I.209 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.209 K.25: 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.26: 6 residues within 4Å: Chain B: K.3, 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.27: 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 K.28: 1 residues within 4Å: Chain B: D.73 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.73, 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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