- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-1-3-mer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADN: ADENOSINE(Non-covalent)
ADN.2: 19 residues within 4Å:- Chain A: H.53, T.55, Q.57, T.58, D.131, E.156, T.157, K.186, D.190, H.315, L.365, L.368, T.372, G.373, H.374, M.379, F.383
- Ligands: NAD.1, ZN.6
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:T.55, A:Q.57, A:E.156, A:T.157, A:T.157, A:K.186, A:K.186, A:H.374
ADN.8: 19 residues within 4Å:- Chain B: H.52, T.54, Q.56, T.57, D.130, E.155, T.156, K.185, D.189, H.314, L.364, L.367, T.371, G.372, H.373, M.378, F.382
- Ligands: NAD.7, ZN.11
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:Q.56, B:E.155, B:T.156, B:K.185, B:K.185, B:H.373
ADN.13: 19 residues within 4Å:- Chain C: H.52, T.54, Q.56, T.57, D.130, E.155, T.156, K.185, D.189, H.314, L.364, L.367, T.371, G.372, H.373, M.378, F.382
- Ligands: NAD.12, ZN.17
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:T.54, C:Q.56, C:T.57, C:T.156, C:T.156, C:K.185, C:K.185, C:H.314, C:H.373
ADN.19: 20 residues within 4Å:- Chain D: I.51, H.52, T.54, Q.56, T.57, D.130, E.155, T.156, K.185, D.189, H.314, L.364, L.367, T.371, G.372, H.373, M.378, F.382
- Ligands: NAD.18, ZN.23
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:Q.56, D:T.57, D:T.156, D:K.185, D:K.185, D:H.373
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 8 residues within 4Å:- Chain A: D.457, T.458, Y.459, R.460
- Chain B: D.456, T.457, Y.458, R.459
6 PLIP interactions:3 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:R.460, B:D.456, B:R.459, B:R.459
- Water bridges: A:R.460, A:R.460
GOL.14: 5 residues within 4Å:- Chain C: T.158, H.161, G.290
- Chain D: Y.444, I.445
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Water bridges: D:Y.444, D:Y.444
- Hydrogen bonds: C:H.161
GOL.20: 5 residues within 4Å:- Chain C: Y.444
- Chain D: T.157, T.158, H.161, G.290
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:Y.444
- Water bridges: C:Y.444, D:T.157, D:G.290
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.4: 4 residues within 4Å:- Chain A: R.17, I.21, E.24
- Chain C: H.351
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:E.24
- Water bridges: A:R.34, A:R.34
- Salt bridges: A:R.17, C:H.351
PO4.9: 4 residues within 4Å:- Chain B: R.16, I.20, E.23
- Chain D: H.351
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain D- Water bridges: B:R.33, B:R.33, B:R.33
- Salt bridges: B:R.16, D:H.351
PO4.15: 4 residues within 4Å:- Chain A: H.352
- Chain C: R.16, I.20, E.23
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Water bridges: C:R.33, C:R.33
- Salt bridges: C:R.16, A:H.352
PO4.21: 4 residues within 4Å:- Chain B: H.351
- Chain D: R.16, I.20, E.23
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Water bridges: D:R.33, D:R.33
- Salt bridges: D:R.16, B:H.351
- 4 x K: POTASSIUM ION(Non-covalent)
K.5: 4 residues within 4Å:- Chain A: Q.57, T.372, G.373, H.374
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.372, A:T.372, A:H.374, H2O.8, H2O.9
K.10: 4 residues within 4Å:- Chain B: Q.56, T.371, G.372, H.373
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.371, B:T.371, B:H.373, H2O.25, H2O.26
K.16: 5 residues within 4Å:- Chain C: Q.56, T.371, G.372, H.373, P.374
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:T.371, C:T.371, C:H.373, H2O.43, H2O.44
K.22: 4 residues within 4Å:- Chain D: Q.56, T.371, G.372, H.373
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:T.371, D:T.371, D:H.373, H2O.64, H2O.65
- 4 x ZN: ZINC ION(Non-covalent)
ZN.6: 6 residues within 4Å:- Chain A: H.53, C.77, D.131, G.132, H.315
- Ligands: ADN.2
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:C.77, A:D.131, A:D.131, A:H.315
ZN.11: 6 residues within 4Å:- Chain B: H.52, C.76, D.130, G.131, H.314
- Ligands: ADN.8
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.76, B:D.130, B:D.130, B:H.314
ZN.17: 6 residues within 4Å:- Chain C: H.52, C.76, D.130, G.131, H.314
- Ligands: ADN.13
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:C.76, C:D.130, C:D.130, C:H.314
ZN.23: 6 residues within 4Å:- Chain D: H.52, C.76, D.130, G.131, H.314
- Ligands: ADN.19
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.76, D:D.130, D:D.130, D:H.314
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Czyrko, J. et al., Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep (2018)
- Release Date
- 2018-08-08
- Peptides
- Adenosylhomocysteinase: A
Adenosylhomocysteinase: BCD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-1-3-mer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADN: ADENOSINE(Non-covalent)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Czyrko, J. et al., Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep (2018)
- Release Date
- 2018-08-08
- Peptides
- Adenosylhomocysteinase: A
Adenosylhomocysteinase: BCD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D