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

Crystal structure of AMP+PPi bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: K.266, S.315, M.322, P.380, Y.381, M.384 Chain B: E.134 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.266, B:E.134 GOL.2: 6 residues within 4Å: Chain A: M.458, T.516, D.517, S.576, L.578, L.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.576, A:S.576 GOL.10: 5 residues within 4Å: Chain A: D.188 Chain B: E.189, Y.193, W.264, N.265 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.189, B:Y.193, B:N.265 GOL.11: 7 residues within 4Å: Chain A: E.134 Chain B: K.266, S.315, M.322, P.380, Y.381, M.384 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.266, A:E.134 GOL.12: 6 residues within 4Å: Chain B: L.55, G.123, R.580, L.583, R.584, Q.600 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.123, B:G.123, B:R.580, B:R.584

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 15 residues within 4Å: Chain A: S.295, R.297, T.298, K.311, R.323, R.390, E.462, N.463, K.479, D.480, E.483, E.484 Ligands: AMP.4, MG.8, MG.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.295, A:T.298 Salt bridges: A:R.297, A:K.311, A:K.311, A:R.323, A:R.390, A:K.479 PPV.13: 12 residues within 4Å: Chain B: S.295, R.297, T.298, K.311, R.390, E.462, N.463, D.480, E.483 Ligands: AMP.14, MG.16, MG.17 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.295, B:T.298, B:R.323, B:D.480 Salt bridges: B:R.297, B:K.311, B:K.311, B:R.390

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 18 residues within 4Å: Chain A: G.172, H.173, N.179, Q.294, S.295, N.318, M.319, R.323, A.407, H.460, E.462, N.463, D.480, E.484 Ligands: PPV.3, SO4.5, MG.8, MG.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.173, A:N.318, A:R.323, A:E.462, A:E.462, A:D.480 Salt bridges: A:R.323, A:H.460 AMP.14: 17 residues within 4Å: Chain B: G.172, H.173, N.179, Q.294, S.295, N.318, M.319, R.323, A.407, H.460, E.462, N.463, D.480, E.484 Ligands: PPV.13, MG.16, MG.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:H.173, B:N.179, B:Q.294, B:N.318, B:R.323, B:E.462, B:E.462, B:N.463, B:E.484 Salt bridges: B:R.323, B:H.460

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

SO4.5: 9 residues within 4Å: Chain A: K.146, M.169, G.172, N.180, R.182, P.195, E.196, Q.294 Ligands: AMP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.172, A:E.196, A:Q.294 Salt bridges: A:K.146, A:R.182 SO4.6: 2 residues within 4Å: Chain A: D.341, R.359 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.359 SO4.7: 4 residues within 4Å: Chain A: Y.451, A.452, D.454, R.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.452 Salt bridges: A:R.562 SO4.15: 7 residues within 4Å: Chain A: E.134, L.183, G.184, F.185 Chain B: N.265, K.266, T.270 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.265, B:T.270, A:G.184 Salt bridges: B:K.266

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 7 residues within 4Å: Chain A: R.297, D.480, E.483, E.484 Ligands: PPV.3, AMP.4, MG.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.480, A:E.483, A:E.484 MG.9: 6 residues within 4Å: Chain A: E.462, N.463, D.480 Ligands: PPV.3, AMP.4, MG.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.462, A:D.480, AMP.4 MG.16: 7 residues within 4Å: Chain B: R.297, D.480, E.483, E.484 Ligands: PPV.13, AMP.14, MG.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.480, B:E.483, B:E.484 MG.17: 6 residues within 4Å: Chain B: E.462, N.463, D.480 Ligands: PPV.13, AMP.14, MG.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.462, B:D.480

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
D

B
E

Desferrioxamine synthetase DesD

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