- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.7: 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.8, MG.9
25 PLIP interactions:25 interactions with chain A- Hydrogen bonds: A:Q.294, A:S.295, A:T.298, A:N.318, A:R.323, A:E.462, A:N.463, A:D.480
- Water bridges: 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:H.460, A:H.460, A:G.461
- Salt bridges: A:R.297, A:K.311, A:K.311, A:R.323, A:R.390, A:H.460
ATP.17: 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.18, MG.19
27 PLIP interactions:27 interactions with chain B- Hydrogen bonds: B:Q.294, B:S.295, B:T.298, B:N.318, B:R.323, B:E.462, B:E.462, B:N.463, B:D.480, B:D.480
- Water bridges: B:G.172, B:G.172, B:G.172, B:H.173, B:R.297, B:R.297, B:R.323, B:R.323, B:H.460, B:H.460, B:G.461
- Salt bridges: B:R.297, B:K.311, B:K.311, B:R.323, B:R.390, B:H.460
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.8: 6 residues within 4Å:- Chain A: R.297, K.311, D.480, E.483, E.484
- Ligands: ATP.7
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.9: 5 residues within 4Å:- Chain A: H.460, E.462, N.463, D.480
- Ligands: ATP.7
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.462, A:D.480
MG.18: 6 residues within 4Å:- Chain B: R.297, K.311, D.480, E.483, E.484
- Ligands: ATP.17
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.8
MG.19: 5 residues within 4Å:- Chain B: H.460, E.462, N.463, D.480
- Ligands: ATP.17
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)
MPD.10: 9 residues within 4Å:- Chain A: L.41, T.143, K.146, L.147, T.170, H.411, V.412, D.413, H.414
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.147, A:T.170
- Hydrogen bonds: A:T.170
MPD.20: 9 residues within 4Å:- Chain B: L.41, T.143, K.146, L.147, T.170, H.411, V.412, D.413, H.414
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.147, B:T.170
- Hydrogen bonds: 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
EB
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 12 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)
- 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
EB
E