SMTL ID : 7tgj.3 (2 other biounits)

Crystal structure of DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: E.189, Y.193, W.264 Chain B: D.188 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.189, A:Y.193, A:Y.193, B:D.188, B:D.188 Water bridges: A:N.265 GOL.5: 4 residues within 4Å: Chain A: D.188 Chain B: E.189, Y.193, W.264 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.193, A:D.188 Water bridges: B:N.265

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

SO4.2: 5 residues within 4Å: Chain A: G.161, F.162, E.401, S.402, L.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.162, A:L.403 SO4.3: 7 residues within 4Å: Chain A: S.295, R.297, T.298, K.311, R.390, N.463, D.480 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.295, A:T.298, A:T.298, A:N.463 Salt bridges: A:R.297, A:K.311, A:R.390, A:K.479 SO4.4: 3 residues within 4Å: Chain A: R.297, R.323, G.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.324 Salt bridges: A:R.297, A:R.323 SO4.6: 5 residues within 4Å: Chain B: G.161, F.162, E.401, S.402, L.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.162, B:L.403 SO4.7: 7 residues within 4Å: Chain B: S.295, R.297, T.298, K.311, R.390, N.463, D.480 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.295, B:T.298, B:T.298, B:N.463 Salt bridges: B:R.297, B:K.311, B:R.390, B:K.479 SO4.8: 3 residues within 4Å: Chain B: R.297, R.323, G.324 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.324 Salt bridges: B:R.297, B:R.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD. J.Biol.Chem. (2022)

Release Date

2022-07-06

Peptides

Desferrioxamine synthetase DesD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

Desferrioxamine synthetase DesD

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