SMTL ID : 7tgk.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: S.31, R.34 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.31, A:S.31 Salt bridges: A:R.34 SO4.2: 4 residues within 4Å: Chain A: V.69, R.71, S.78, R.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.78 Salt bridges: A:R.71, A:R.80 SO4.3: 5 residues within 4Å: Chain A: R.86, A.531, A.537, E.538 Ligands: MPD.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.538 Salt bridges: A:R.86 SO4.4: 5 residues within 4Å: Chain A: A.87, E.538, D.539, W.542, P.608 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.538 SO4.5: 4 residues within 4Å: Chain A: D.113, I.116, E.117 Chain B: A.373 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain A: G.161, F.162, L.397, S.402, L.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.162, A:L.403 Water bridges: A:Q.163 SO4.7: 6 residues within 4Å: Chain A: F.176, M.458, D.517, L.578, L.581, V.590 No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain A: H.209, R.277, Q.278, N.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.278 Salt bridges: A:H.209 SO4.9: 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 SO4.10: 3 residues within 4Å: Chain A: D.560, F.563, R.564 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.564 SO4.11: 2 residues within 4Å: Chain A: P.150, Q.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151 SO4.19: 1 residues within 4Å: Chain B: R.34 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.31, B:S.31 Salt bridges: B:R.34 SO4.20: 2 residues within 4Å: Chain B: R.499, R.502 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.499, B:R.502 SO4.21: 7 residues within 4Å: Chain B: F.176, M.458, D.517, L.578, L.581, V.590, L.599 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.517

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.12: 25 residues within 4Å: Chain A: G.172, H.173, P.174, N.179, Q.294, S.295, I.296, R.297, T.298, K.311, N.318, M.319, R.323, R.390, A.407, H.460, G.461, E.462, N.463, K.479, D.480, E.483, E.484 Ligands: MG.13, MG.14 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:S.295, A:T.298, A:N.318, A:R.323, A:E.462, A:N.463, A:D.480, A:D.480 Water bridges: A:G.172, A:G.172, A:H.173, A:R.297, A:R.297, A:R.323, A:G.461, A:G.461, A:G.461 Salt bridges: A:R.297, A:K.311, A:K.311, A:R.323, A:R.390, A:H.460, A:K.479 ATP.22: 25 residues within 4Å: Chain B: G.172, H.173, P.174, N.179, Q.294, S.295, I.296, R.297, T.298, K.311, N.318, M.319, R.323, R.390, A.407, H.460, G.461, E.462, N.463, K.479, D.480, E.483, E.484 Ligands: MG.23, MG.24 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.179, B:Q.294, B:T.298, B:N.318, B:R.323, B:E.462, B:E.462, B:N.463 Water bridges: B:G.172, B:H.173, B:G.461 Salt bridges: B:R.297, B:K.311, B:K.311, B:R.323, B:R.390, B:H.460, B:K.479

4 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain A: R.297, K.311, D.480, E.483, E.484 Ligands: ATP.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.480, A:D.480, A:E.483, A:E.484, H2O.3 MG.14: 6 residues within 4Å: Chain A: H.460, E.462, N.463, K.479, D.480 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.462, A:D.480 MG.23: 6 residues within 4Å: Chain B: R.297, K.311, D.480, E.483, E.484 Ligands: ATP.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.480, B:D.480, B:E.483, B:E.484 MG.24: 6 residues within 4Å: Chain B: H.460, E.462, N.463, K.479, D.480 Ligands: ATP.22 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.462, B:D.480

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.15: 7 residues within 4Å: Chain A: D.341, D.345, K.351, S.356, I.357, R.359, E.391 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.345, A:K.351, A:R.359, A:R.359 B3P.25: 5 residues within 4Å: Chain B: D.73, R.119, H.120, D.126, E.127 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.120, B:D.126, B:E.127 Water bridges: B:D.126, B:D.126

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.16: 11 residues within 4Å: Chain A: E.37, L.41, T.143, K.146, L.147, Q.151, T.170, H.411, V.412, D.413, H.414 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.41, A:H.414 Hydrogen bonds: A:T.170, A:T.170 MPD.17: 5 residues within 4Å: Chain A: E.415, G.416, R.417, E.533, E.534 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.416 MPD.18: 6 residues within 4Å: Chain A: A.531, E.534, V.535, L.536, A.537 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.534 MPD.26: 7 residues within 4Å: Chain A: D.188 Chain B: D.188, E.189, Y.193, W.261, W.264, N.265 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.189, B:W.264, B:W.264 MPD.27: 9 residues within 4Å: Chain B: L.41, T.143, K.146, L.147, T.170, H.411, V.412, D.413, H.414 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.147, B:T.170

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
C

Desferrioxamine synthetase DesD

Related Entries With Identical Sequence