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

Crystal structure of HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: W.35, E.36, P.108, L.109, A.110 Chain B: R.277 Ligand excluded by PLIP GOL.2: 8 residues within 4Å: Chain A: K.266, S.315, M.322, P.380, Y.381, M.384 Chain B: E.134 Ligands: GOL.36 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: K.146, M.169, T.170, G.172, N.180, R.182, E.196, Q.294 Ligands: LMS.15 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: G.161, F.162, V.394, S.402, L.403 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: Y.223, A.224, R.228, D.240 Ligands: SO4.22 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: E.306, K.307, H.308, E.391, S.392 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: E.189, Y.193, W.264 Chain B: D.188 Ligands: SO4.18, SO4.47 Ligand excluded by PLIP GOL.8: 9 residues within 4Å: Chain A: L.42, K.45, T.139, T.143, T.170, E.171, V.177, N.179, N.180 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: L.122, G.123, R.580, R.584, Q.600 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: F.321, E.484 Ligands: I3U.14, LMS.15 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain A: E.134, L.183, G.184, F.185 Chain B: N.265, K.266, V.269, T.270 Ligands: GOL.26 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: R.210, S.211, R.212, A.213, A.214, R.367 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: H.20, D.188 Chain B: Y.193, W.264 Ligands: SO4.18, SO4.47 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain A: E.134 Chain B: K.266, M.322, P.380, Y.381, M.384 Ligands: GOL.11 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: L.55, G.123, R.580, R.584, Q.600 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain B: L.158, G.400, S.402, R.426, L.468, K.469, D.470, G.471 Ligand excluded by PLIP GOL.29: 10 residues within 4Å: Chain B: K.146, E.166, M.169, G.172, N.180, R.182, P.195, E.196, Q.294 Ligands: LMS.41 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: Y.145, T.148, K.149, P.150 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain A: E.370, A.373 Chain B: R.100, R.102, D.113, I.116, E.117 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain B: R.584, D.585, Q.588, M.589, V.590, D.591 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain B: F.321, R.323, E.484 Ligands: I3U.40, LMS.41 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain B: Y.453, V.493, L.494 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain B: L.42, K.45, T.143, T.170, E.171, F.176, V.177, N.179, N.180 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain A: N.265, K.266, V.269, T.270 Chain B: E.134, L.183, G.184, F.185 Ligands: GOL.2 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain B: E.306, K.307, H.308, E.391, S.392 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain B: L.183, G.184, S.315, M.322, R.587 Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain B: R.377, R.382 Ligand excluded by PLIP

2 x I3U: 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid(Non-covalent)

I3U.14: 10 residues within 4Å: Chain A: F.176, M.319, F.321, R.323, H.460, D.517, L.581, M.589 Ligands: GOL.10, LMS.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.323, A:R.323, A:D.517 I3U.40: 9 residues within 4Å: Chain B: F.176, M.319, F.321, R.323, D.517, L.581, M.589 Ligands: GOL.33, LMS.41 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.581 Hydrogen bonds: B:R.323, B:R.323, B:D.517

2 x LMS: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE(Non-covalent)

LMS.15: 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: GOL.3, GOL.10, I3U.14, MG.17 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.318, A:R.323, A:H.460, A:E.462, A:N.463 Water bridges: A:R.297, A:R.323, A:R.323, A:G.461 Salt bridges: A:R.323, A:H.460 LMS.41: 18 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: GOL.29, GOL.33, I3U.40, MG.43 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.173, B:Q.294, B:N.318, B:R.323, B:H.460, B:E.462, B:E.462, B:N.463, B:D.480 Water bridges: B:R.297, B:R.323, B:R.323 Salt bridges: B:R.323, B:H.460

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 10 residues within 4Å: Chain A: S.295, R.297, T.298, K.311, R.390, E.462, N.463, K.479, D.480 Ligands: MG.17 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.295, A:S.295, A:T.298 Water bridges: A:R.297, A:R.297 Salt bridges: A:R.297, A:K.311, A:R.390, A:K.479 PO4.42: 10 residues within 4Å: Chain B: S.295, R.297, T.298, K.311, R.390, E.462, N.463, K.479, D.480 Ligands: MG.43 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.295, B:R.297, B:T.298 Water bridges: B:R.297 Salt bridges: B:K.311, B:R.390, B:K.479

2 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain A: E.462, N.463, D.480 Ligands: LMS.15, PO4.16 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.462, A:D.480, LMS.15 MG.43: 5 residues within 4Å: Chain B: E.462, N.463, D.480 Ligands: LMS.41, PO4.42 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.462, B:D.480, LMS.41

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

SO4.18: 4 residues within 4Å: Chain A: H.20, D.188 Ligands: GOL.7, GOL.13 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: D.585, Q.588, M.589, D.591 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain A: R.71, S.72, D.73, D.74, G.75 Ligands: SO4.25 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: L.423, R.426, D.470, G.471 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain A: R.228 Ligands: GOL.5 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: Y.451, A.452, D.454, R.562 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: D.73, R.119, H.120 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain A: T.57, E.59, V.69, V.70, R.71 Ligands: SO4.20 Ligand excluded by PLIP SO4.44: 1 residues within 4Å: Chain B: R.34 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain B: G.161, F.162, S.402, L.403 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain B: R.210, F.215, Y.223 Ligand excluded by PLIP SO4.47: 6 residues within 4Å: Chain B: D.188, E.189, A.192, Y.193 Ligands: GOL.7, GOL.13 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain B: E.33, R.34, E.37, L.147 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain B: R.54, D.89 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain B: L.231, G.232, D.288, H.304, K.307 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain B: A.531, E.534, V.535, L.536, A.537 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain B: R.550, Q.553, F.569, L.612 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain B: F.56, T.57, V.69, V.70, R.71 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain B: A.452, D.454, R.562 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain B: S.352, T.353, G.354, Q.474 Ligand excluded by PLIP

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
A

B
B

Desferrioxamine synthetase DesD

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