SMTL ID : 7rbx.1

Crystal structure of isocitrate lyase and phosphorylmutase:isocitrate lyase from Brucella melitensis biovar Abortus 2308 bound to itaconic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: A.113, R.137 Chain B: A.113, R.137 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.137, B:R.137 EDO.5: 6 residues within 4Å: Chain A: L.62, K.136, R.140, Q.143, A.189 Chain C: E.188 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.189, C:E.188 Water bridges: A:Q.143 EDO.6: 2 residues within 4Å: Chain A: D.48 Chain C: L.424 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.425 EDO.7: 5 residues within 4Å: Chain A: E.188 Chain C: L.62, K.136, R.140, A.189 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.140, C:A.189, A:E.188 Water bridges: A:Y.60 EDO.10: 4 residues within 4Å: Chain C: A.113, R.137 Chain D: A.113, R.137 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:R.137, D:R.137 EDO.16: 5 residues within 4Å: Chain B: E.188 Chain D: K.136, R.140, Q.143, A.189 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:A.189, B:E.188 Water bridges: D:Q.143

4 x ITN: 2-methylidenebutanedioic acid(Covalent)

ITN.2: 13 residues within 4Å: Chain A: W.107, D.122, D.168, C.206, G.207, H.208, R.243, E.302, N.330, S.332, S.334, T.364 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.364 Hydrogen bonds: A:G.207, A:E.302, A:E.302, A:N.330, A:S.332, A:S.334 Water bridges: A:G.106, A:K.204, A:R.243 Salt bridges: A:K.204, A:H.208, A:R.243 ITN.8: 13 residues within 4Å: Chain B: W.107, D.122, D.168, C.206, G.207, H.208, R.243, E.302, N.330, S.332, S.334, T.364 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.364 Hydrogen bonds: B:G.207, B:N.330, B:N.330, B:S.332, B:S.334, B:T.364 Water bridges: B:Y.103, B:G.106, B:K.204, B:R.243 Salt bridges: B:K.204, B:H.208, B:R.243 ITN.11: 13 residues within 4Å: Chain C: W.107, D.122, D.168, C.206, G.207, H.208, R.243, E.302, N.330, S.332, S.334, T.364 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.364 Hydrogen bonds: C:G.207, C:E.302, C:N.330, C:N.330, C:S.332, C:S.334, C:T.364 Water bridges: C:K.204, C:R.243 Salt bridges: C:K.204, C:H.208, C:R.243 ITN.14: 13 residues within 4Å: Chain D: W.107, D.122, D.168, C.206, G.207, H.208, R.243, E.302, N.330, S.332, S.334, T.364 Ligands: MG.13 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:T.364 Hydrogen bonds: D:G.207, D:E.302, D:N.330, D:S.332, D:S.334 Water bridges: D:G.106, D:K.204, D:R.243 Salt bridges: D:K.204, D:H.208, D:R.243

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.122, D.168 Ligands: ITN.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.168, H2O.1, H2O.2, H2O.3 MG.9: 4 residues within 4Å: Chain B: D.122, D.168, K.204 Ligands: ITN.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.168, H2O.16, H2O.17, H2O.20 MG.12: 3 residues within 4Å: Chain C: D.122, D.168 Ligands: ITN.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.168, H2O.31, H2O.34, H2O.34 MG.13: 3 residues within 4Å: Chain D: D.122, D.168 Ligands: ITN.14 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.168, H2O.47, H2O.48, H2O.49

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: G.269, R.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.270 Salt bridges: A:R.270 SO4.15: 3 residues within 4Å: Chain A: I.256 Chain D: G.269, R.270 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.270 Salt bridges: D:R.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demars, A. et al., Aconitate decarboxylase 1 participates in the control of pulmonary Brucella infection in mice. Plos Pathog. (2021)

Release Date

2021-10-06

Peptides

Isocitrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrase