- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 24 x GOL: GLYCEROL(Non-functional Binders)
- 2 x I3U: 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid(Non-covalent)
I3U.10: 8 residues within 4Å:- Chain A: F.176, M.319, F.321, R.323, D.517, L.581
- Ligands: GOL.5, LMS.11
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.323, A:R.323, A:D.517
I3U.39: 11 residues within 4Å:- Chain B: F.176, M.319, F.321, R.323, M.458, D.517, L.581, M.589, V.590
- Ligands: GOL.38, LMS.40
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.11: 19 residues within 4Å:- Chain A: G.172, H.173, N.179, Q.294, S.295, I.296, N.318, M.319, R.323, A.407, H.460, E.462, N.463, D.480, E.484
- Ligands: GOL.4, GOL.5, I3U.10, MG.13
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:H.173, A:Q.294, A:N.318, A:H.460, A:E.462, A:E.462, A:N.463
- Water bridges: A:R.323, A:R.323, A:G.461
- Salt bridges: A:R.323, A:H.460
LMS.40: 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.38, I3U.39, MG.42
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:Q.294, B:N.318, B:R.323, B:H.460, B:E.462, B:N.463, B:D.480
- Water bridges: B:G.172, B:G.461, B:G.461
- Salt bridges: B:R.323, B:H.460
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.12: 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.13
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
PO4.41: 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.42
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:S.295, B:T.298, 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.13: 5 residues within 4Å:- Chain A: E.462, N.463, D.480
- Ligands: LMS.11, PO4.12
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:E.462, A:D.480, LMS.11
MG.42: 5 residues within 4Å:- Chain B: E.462, N.463, D.480
- Ligands: LMS.40, PO4.41
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:E.462, B:D.480, LMS.40
- 20 x SO4: SULFATE ION(Non-functional Binders)
SO4.14: 5 residues within 4Å:- Chain A: S.72, D.73, D.74, G.75
- Ligands: SO4.22
Ligand excluded by PLIPSO4.15: 4 residues within 4Å:- Chain A: L.183, L.317, M.322, R.587
Ligand excluded by PLIPSO4.16: 5 residues within 4Å:- Chain A: H.209, Y.253, R.277, Q.278, N.279
Ligand excluded by PLIPSO4.17: 1 residues within 4Å:- Chain A: R.502
Ligand excluded by PLIPSO4.18: 3 residues within 4Å:- Chain A: G.123, L.124, S.125
Ligand excluded by PLIPSO4.19: 7 residues within 4Å:- Chain A: G.161, F.162, L.397, E.401, S.402, L.403
- Ligands: SO4.20
Ligand excluded by PLIPSO4.20: 5 residues within 4Å:- Chain A: G.161, F.162, Q.163, F.300
- Ligands: SO4.19
Ligand excluded by PLIPSO4.21: 6 residues within 4Å:- Chain A: L.158, L.423, R.426, L.468, D.470, G.471
Ligand excluded by PLIPSO4.22: 6 residues within 4Å:- Chain A: T.57, E.59, V.69, V.70, R.71
- Ligands: SO4.14
Ligand excluded by PLIPSO4.23: 5 residues within 4Å:- Chain A: Y.223, D.240, P.250, Y.253, L.255
Ligand excluded by PLIPSO4.43: 3 residues within 4Å:- Chain B: L.183, R.587
- Ligands: GOL.24
Ligand excluded by PLIPSO4.44: 3 residues within 4Å:- Chain B: R.71, S.78, R.80
Ligand excluded by PLIPSO4.45: 6 residues within 4Å:- Chain B: G.161, F.162, L.397, E.401, S.402, L.403
Ligand excluded by PLIPSO4.46: 3 residues within 4Å:- Chain B: D.341, R.342, D.345
Ligand excluded by PLIPSO4.47: 1 residues within 4Å:- Chain B: R.499
Ligand excluded by PLIPSO4.48: 1 residues within 4Å:- Chain B: R.34
Ligand excluded by PLIPSO4.49: 2 residues within 4Å:- Chain B: E.534, V.535
Ligand excluded by PLIPSO4.50: 4 residues within 4Å:- Chain B: L.423, R.426, D.470, G.471
Ligand excluded by PLIPSO4.51: 7 residues within 4Å:- Chain B: D.454, M.488, D.489, K.510, R.562, Y.566
- Ligands: SO4.52
Ligand excluded by PLIPSO4.52: 4 residues within 4Å:- Chain B: Y.451, D.454, R.562
- Ligands: SO4.51
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
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 24 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)
- 20 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
CB
D