SMTL ID : 9jpi.1

The complex structure of DHAD with aspterric acid (AA).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.104, D.146, K.147, T.222, E.469 Ligands: K0O.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.104, A:D.146, A:E.469 MG.6: 6 residues within 4Å: Chain B: D.104, D.146, K.147, T.222, E.469 Ligands: K0O.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.104, B:D.146, B:E.469

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

SO4.2: 4 residues within 4Å: Chain A: T.110, R.111 Chain B: R.31, W.135 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.111 Salt bridges: A:R.111, B:R.31 SO4.7: 4 residues within 4Å: Chain A: R.31, W.135 Chain B: T.110, R.111 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.111 Salt bridges: B:R.111, A:R.31

4 x K0O: Aspterric Acid(Non-covalent)

K0O.3: 15 residues within 4Å: Chain A: D.104, M.108, D.146, I.183, V.184, F.187, C.217, Y.221, T.222, N.295, E.469, L.471, S.495 Ligands: MG.1, FES.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.183, A:I.183, A:V.184, A:F.187, A:F.187, A:F.187, A:Y.221, A:L.471 Hydrogen bonds: A:D.146, A:T.222, A:T.222, A:N.295 Water bridges: A:A.223 K0O.4: 10 residues within 4Å: Chain A: R.111, C.114, F.115, P.465, K.556, L.562 Chain B: A.13, D.14, P.15, S.16 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.111, A:F.115, A:K.556, A:L.562 Hydrogen bonds: B:S.16, B:S.16 K0O.8: 15 residues within 4Å: Chain B: D.104, M.108, D.146, I.183, V.184, F.187, C.217, Y.221, T.222, N.295, E.469, L.471, S.495 Ligands: MG.6, FES.10 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.183, B:I.183, B:V.184, B:F.187, B:F.187, B:F.187, B:Y.221, B:L.471 Hydrogen bonds: B:D.146, B:T.222, B:N.295 Water bridges: B:A.223 K0O.9: 10 residues within 4Å: Chain A: A.13, D.14, P.15, S.16 Chain B: R.111, C.114, F.115, P.465, K.556, L.562 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.16, A:S.16 Hydrophobic interactions: B:R.111, B:F.115, B:K.556, B:L.562

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.5: 10 residues within 4Å: Chain A: N.70, C.72, D.104, A.105, C.145, D.146, A.216, C.217, A.223 Ligands: K0O.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.72, A:C.145, A:C.217, H2O.1 FES.10: 10 residues within 4Å: Chain B: N.70, C.72, D.104, A.105, C.145, D.146, A.216, C.217, A.223 Ligands: K0O.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.72, B:C.145, B:C.217, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zang, X. et al., Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance. Biodes Res (2024)

Release Date

2024-12-04

Peptides

Dihydroxy-acid dehydratase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dihydroxy-acid dehydratase, chloroplastic