- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
ZN.2: 6 residues within 4Å:- Chain A: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.5
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:C.88, A:D.142, A:D.142
ZN.7: 6 residues within 4Å:- Chain B: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.10
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:C.88, B:D.142, B:D.142
ZN.12: 6 residues within 4Å:- Chain C: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.15
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:C.88, C:D.142, C:D.142
ZN.17: 6 residues within 4Å:- Chain D: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.21
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:C.88, D:D.142, D:D.142
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain C: H.363
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:E.35, A:E.35
- Water bridges: A:R.45, A:R.45
- Salt bridges: A:R.28, C:H.363
PO4.8: 4 residues within 4Å:- Chain B: R.28, I.32, E.35
- Chain D: H.363
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain D- Water bridges: B:E.35, B:R.45, B:R.45
- Salt bridges: B:R.28, D:H.363
PO4.13: 4 residues within 4Å:- Chain A: H.363
- Chain C: R.28, I.32, E.35
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Water bridges: C:R.45, C:R.45
- Salt bridges: C:R.28, A:H.363
PO4.18: 4 residues within 4Å:- Chain B: H.363
- Chain D: R.28, I.32, E.35
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Water bridges: D:R.45, D:R.45
- Salt bridges: D:R.28, B:H.363
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.4: 31 residues within 4Å:- Chain A: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385
- Chain B: L.449, Q.453, K.466, Y.470
- Ligands: ADN.5
27 PLIP interactions:21 interactions with chain A, 6 interactions with chain B- Hydrophobic interactions: A:N.202, A:V.235
- Hydrogen bonds: A:T.169, A:T.169, A:T.170, A:T.170, A:T.170, A:N.202, A:G.233, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:H.326, A:N.378, A:N.378, B:Q.453, B:Q.453, B:K.466, B:K.466
- Water bridges: A:N.192, A:G.236, A:F.327, A:E.330, B:T.450
- Salt bridges: B:K.466
NAD.9: 31 residues within 4Å:- Chain A: L.449, Q.453, K.466, Y.470
- Chain B: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385
- Ligands: ADN.10
26 PLIP interactions:20 interactions with chain B, 6 interactions with chain A- Hydrophobic interactions: B:N.202, B:V.235
- Hydrogen bonds: B:T.169, B:T.169, B:T.169, B:T.170, B:N.202, B:G.233, B:D.234, B:V.235, B:V.255, B:D.256, B:N.303, B:H.326, B:N.378, B:N.378, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470
- Water bridges: B:N.192, B:G.236, B:F.327, B:E.330
NAD.14: 31 residues within 4Å:- Chain C: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385
- Chain D: L.449, Q.453, K.466, Y.470
- Ligands: ADN.15
27 PLIP interactions:22 interactions with chain C, 5 interactions with chain D- Hydrophobic interactions: C:N.202, C:V.235
- Hydrogen bonds: C:T.169, C:T.169, C:T.170, C:T.170, C:T.170, C:N.202, C:G.233, C:D.234, C:V.235, C:V.255, C:D.256, C:N.303, C:H.326, C:N.378, C:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466, D:Y.470
- Water bridges: C:N.192, C:D.234, C:G.236, C:F.327, C:E.330
NAD.20: 30 residues within 4Å:- Chain C: Q.453, K.466, Y.470
- Chain D: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385
- Ligands: ADN.21
28 PLIP interactions:7 interactions with chain C, 21 interactions with chain D- Hydrogen bonds: C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470, C:Y.470, D:T.169, D:T.170, D:T.170, D:T.170, D:N.202, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:H.326, D:N.378, D:N.378
- Salt bridges: C:K.466
- Hydrophobic interactions: D:N.202, D:V.235
- Water bridges: D:G.233, D:D.234, D:D.234, D:G.236, D:F.327, D:E.330
- 4 x ADN: ADENOSINE(Non-covalent)
ADN.5: 19 residues within 4Å:- Chain A: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: ZN.2, NAD.4
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:E.167, A:T.168, A:T.168, A:K.197, A:K.197, A:H.326, A:H.385
ADN.10: 19 residues within 4Å:- Chain B: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: ZN.7, NAD.9
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:Q.68, B:E.167, B:T.168, B:K.197, B:K.197, B:H.326, B:H.385
ADN.15: 19 residues within 4Å:- Chain C: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: ZN.12, NAD.14
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:T.66, C:Q.68, C:T.69, C:T.168, C:T.168, C:K.197, C:K.197, C:H.326, C:H.385
ADN.21: 19 residues within 4Å:- Chain D: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: ZN.17, NAD.20
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:Q.68, D:T.69, D:T.168, D:K.197, D:K.197, D:H.326, D:H.385
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADN: ADENOSINE(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D