- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.9: 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.10, MG.11
28 PLIP interactions:28 interactions with chain A- Hydrogen bonds: A:S.295, A:T.298, A:N.318, A:R.323, A:E.462, A:E.462, A:N.463, A:D.480, A:D.480
- Water bridges: A:G.172, A:G.172, A:G.172, A:G.172, A:G.172, A:H.173, A:R.297, A:R.297, A:R.323, A:R.323, 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.24: 24 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
- Ligands: MG.25, MG.26
21 PLIP interactions:21 interactions with chain B- Hydrogen bonds: B:S.295, B:T.298, B:N.318, B:R.323, B:E.462, B:N.463
- Water bridges: B:G.172, B:G.172, B:H.173, B:R.297, B:R.297, B:R.323, B:G.461, 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.10: 6 residues within 4Å:- Chain A: R.297, K.311, D.480, E.483, E.484
- Ligands: ATP.9
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.11: 6 residues within 4Å:- Chain A: H.460, E.462, N.463, K.479, D.480
- Ligands: ATP.9
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.462, A:D.480
MG.25: 6 residues within 4Å:- Chain B: R.297, K.311, D.480, E.483, E.484
- Ligands: ATP.24
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.480, B:D.480, B:E.483, B:E.484, H2O.11
MG.26: 6 residues within 4Å:- Chain B: H.460, E.462, N.463, K.479, D.480
- Ligands: ATP.24
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.462, B:D.480
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
- 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
BB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
- 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
BB
A