- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.89 Å
- Oligo State
- homo-dimer
- Ligands
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PPV: PYROPHOSPHATE(Non-covalent)
PPV.3: 13 residues within 4Å:- Chain A: S.295, R.297, T.298, K.311, R.323, R.390, E.462, N.463, D.480, E.483
- Ligands: AMP.4, MG.6, MG.7
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:S.295, A:R.323, A:D.480
- Salt bridges: A:R.297, A:K.311, A:K.311, A:R.390, A:K.479
PPV.13: 14 residues within 4Å:- Chain B: S.295, R.297, T.298, K.311, R.323, R.390, E.462, N.463, K.479, D.480, E.483
- Ligands: AMP.14, MG.18, MG.19
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:S.295, B:T.298, B:N.463
- Salt bridges: B:R.297, B:K.311, B:K.311, B:R.323, B:R.390, B:K.479
- 2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
AMP.4: 19 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, G.461, E.462, N.463, D.480, E.484
- Ligands: PPV.3, SO4.5, MG.6, MG.7
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:H.173, A:Q.294, A:N.318, A:R.323, A:G.461, A:E.462, A:N.463
- Salt bridges: A:R.323, A:H.460
AMP.14: 19 residues within 4Å:- Chain B: G.172, H.173, N.179, Q.294, S.295, N.318, M.319, R.323, A.407, M.458, H.460, E.462, N.463, D.480, E.484
- Ligands: PPV.13, SO4.16, MG.18, MG.19
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:H.173, B:Q.294, B:N.318, B:R.323, B:E.462, B:E.462, B:N.463, B:D.480, B:E.484, B:E.484
- Salt bridges: B:R.323, B:H.460
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 10 residues within 4Å:- Chain A: K.146, M.169, T.170, 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:M.169, A:E.196, A:Q.294
- Salt bridges: A:K.146, A:R.182
SO4.15: 6 residues within 4Å:- Chain A: E.134
- Chain B: K.266, S.315, P.380, Y.381, M.384
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.315, B:Y.381
- Salt bridges: B:K.266
SO4.16: 10 residues within 4Å:- Chain B: K.146, E.166, M.169, T.170, G.172, R.182, P.195, E.196, Q.294
- Ligands: AMP.14
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.196, B:Q.294
- Salt bridges: B:K.146, B:R.182
SO4.17: 5 residues within 4Å:- Chain B: E.306, H.308, E.391, S.392, P.395
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.306, B:S.392
- Salt bridges: B:H.308
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.6: 7 residues within 4Å:- Chain A: R.297, D.480, E.483, E.484
- Ligands: PPV.3, AMP.4, MG.7
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.480, A:E.483, A:E.484
MG.7: 7 residues within 4Å:- Chain A: H.460, E.462, N.463, D.480
- Ligands: PPV.3, AMP.4, MG.6
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:E.462, A:D.480, AMP.4
MG.18: 5 residues within 4Å:- Chain B: D.480, E.483, E.484
- Ligands: PPV.13, AMP.14
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.480, B:D.480, B:E.483, B:E.484
MG.19: 5 residues within 4Å:- Chain B: E.462, N.463, D.480
- Ligands: PPV.13, AMP.14
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
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.89 Å
- Oligo State
- homo-dimer
- Ligands
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PPV: PYROPHOSPHATE(Non-covalent)
- 2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(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
AB
B