- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 2 x I3U: 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid(Non-covalent)
I3U.9: 9 residues within 4Å:- Chain A: F.176, M.319, F.321, R.323, D.517, L.581, M.589, V.590
- Ligands: LMS.10
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:F.321
- Hydrogen bonds: A:R.323, A:R.323, A:D.517
I3U.28: 9 residues within 4Å:- Chain B: F.176, M.319, F.321, R.323, D.517, L.581, M.589, V.590
- Ligands: LMS.29
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.321
- 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.10: 16 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: I3U.9, MG.12
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:N.318, A:R.323, A:H.460, A:E.462, A:N.463
- Salt bridges: A:R.323, A:H.460
LMS.29: 16 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: I3U.28, MG.31
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:N.318, B:R.323, B:H.460, B:E.462, B:E.462, B:N.463, B:D.480
- Salt bridges: B:R.323, B:H.460
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.11: 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.12
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:S.295, A:S.295, A:T.298
- Salt bridges: A:R.297, A:K.311, A:R.390, A:K.479
PO4.30: 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.31
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:S.295, B:S.295, B:T.298
- Salt bridges: B:R.297, B:K.311, B:R.390, B:K.479
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.12: 5 residues within 4Å:- Chain A: E.462, N.463, D.480
- Ligands: LMS.10, PO4.11
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:E.462, A:D.480, LMS.10
MG.31: 5 residues within 4Å:- Chain B: E.462, N.463, D.480
- Ligands: LMS.29, PO4.30
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:E.462, B:D.480, LMS.29
- 14 x SO4: SULFATE ION(Non-functional Binders)
SO4.13: 4 residues within 4Å:- Chain A: L.158, L.423, R.426, G.471
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.471
- Salt bridges: A:R.426
SO4.14: 4 residues within 4Å:- Chain A: S.22, L.23, T.24
- Chain B: G.284
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.23, A:T.24, A:T.24
SO4.15: 3 residues within 4Å:- Chain A: L.147, K.149, Q.151
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.147, A:Q.151
SO4.16: 8 residues within 4Å:- Chain A: L.42, K.45, T.139, T.143, T.170, E.171, V.177, N.179
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:T.143, A:T.170, A:N.179, A:N.180
- Water bridges: A:K.146
- Salt bridges: A:K.45
SO4.17: 6 residues within 4Å:- Chain A: G.161, F.162, L.397, E.401, S.402, L.403
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:F.162, A:L.403
SO4.18: 4 residues within 4Å:- Chain A: Y.223, D.240, Y.253, L.255
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.240
- Water bridges: A:R.228
SO4.19: 6 residues within 4Å:- Chain A: E.306, K.307, H.308, E.391, S.392, P.395
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.306, A:S.392
- Salt bridges: A:H.308
SO4.32: 4 residues within 4Å:- Chain B: L.158, L.423, R.426, G.471
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:G.471
- Salt bridges: B:R.426
SO4.33: 4 residues within 4Å:- Chain A: G.284
- Chain B: S.22, L.23, T.24
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.23, B:T.24, B:T.24
SO4.34: 3 residues within 4Å:- Chain B: L.147, K.149, Q.151
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:L.147, B:Q.151
SO4.35: 8 residues within 4Å:- Chain B: L.42, K.45, T.139, T.143, T.170, E.171, V.177, N.179
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:T.170, B:N.179, B:N.180
- Water bridges: B:K.146
- Salt bridges: B:K.45
SO4.36: 6 residues within 4Å:- Chain B: G.161, F.162, L.397, E.401, S.402, L.403
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:F.162, B:L.403
SO4.37: 4 residues within 4Å:- Chain B: Y.223, D.240, Y.253, L.255
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.223, B:D.240
- Water bridges: B:R.228
SO4.38: 6 residues within 4Å:- Chain B: E.306, K.307, 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
- 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 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 2 x I3U: 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid(Non-covalent)
- 2 x LMS: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 14 x SO4: SULFATE ION(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