SMTL ID : 7tgj.2 (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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.71, S.78, R.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.71, A:S.78, A:S.78, A:R.80, A:R.80 GOL.2: 2 residues within 4Å: Chain A: R.277 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) GOL.3: 6 residues within 4Å: Chain A: H.209, Y.253, R.277, Q.278, N.279 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.279 Water bridges: A:S.211, A:S.211 GOL.4: 2 residues within 4Å: Chain A: S.31, R.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.34 GOL.5: 7 residues within 4Å: Chain A: Y.223, V.236, D.240, L.243, P.250, Y.253, L.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.240, A:P.250 GOL.12: 5 residues within 4Å: Chain B: H.209, Y.253, R.277, Q.278, N.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.253 GOL.13: 5 residues within 4Å: Chain A: D.188 Chain B: D.188, E.189, Y.193, W.264 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.188, B:E.189, B:Y.193, B:W.264, A:D.188

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

SO4.6: 4 residues within 4Å: Chain A: R.86, A.531, A.537, E.538 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.538 Salt bridges: A:R.86 SO4.7: 4 residues within 4Å: Chain A: G.161, F.162, S.402, L.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.162, A:L.403 SO4.8: 6 residues within 4Å: Chain A: S.295, R.297, T.298, K.311, R.390, D.480 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.295, A:D.480 Salt bridges: A:R.297, A:K.311, A:R.390, A:K.479 SO4.9: 4 residues within 4Å: Chain A: G.320, F.321, M.322, P.380 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.320, A:M.322 SO4.10: 3 residues within 4Å: Chain A: G.354, Q.474, R.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.474 SO4.11: 3 residues within 4Å: Chain A: R.297, R.323, G.324 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.297, A:G.324 Water bridges: A:N.318 Salt bridges: A:R.323 SO4.14: 5 residues within 4Å: Chain B: G.161, F.162, L.397, S.402, L.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.162, B:L.403 SO4.15: 5 residues within 4Å: Chain B: R.80, T.101, R.102, D.103, G.104 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.78, B:T.101, B:T.101, B:D.103, B:G.104 Salt bridges: B:R.80 SO4.16: 8 residues within 4Å: Chain B: S.295, R.297, T.298, K.311, R.390, N.463, K.479, D.480 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.295, B:T.298 Salt bridges: B:R.297, B:K.311, B:R.390, B:K.479 SO4.17: 3 residues within 4Å: Chain B: R.297, R.323, G.324 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.324, 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
C

B
D

Desferrioxamine synthetase DesD

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