- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
ADE.2: 12 residues within 4Å:- Chain A: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.1, PO4.10
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385
ADE.14: 12 residues within 4Å:- Chain B: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.13, PO4.20
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.385
ADE.24: 12 residues within 4Å:- Chain C: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.23, PO4.28
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.68, C:T.69, C:H.385
ADE.32: 13 residues within 4Å:- Chain D: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.31, K.35, PO4.37
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.68, D:H.385
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 5 x R9V: (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol(Non-covalent)
R9V.4: 5 residues within 4Å:- Chain A: R.174, F.327, N.329
- Chain D: Y.456
- Ligands: GOL.5
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:R.174, A:F.327, A:F.327, A:F.327
- pi-Cation interactions: A:R.174, A:F.327
R9V.6: 4 residues within 4Å:- Chain A: Y.456
- Chain D: R.174, F.327, N.329
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:R.174, D:F.327, D:F.327
- Water bridges: D:N.329
- pi-Cation interactions: D:R.174
R9V.17: 4 residues within 4Å:- Chain B: R.174, F.327, N.329
- Chain C: Y.456
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:R.174, B:F.327, B:F.327, B:F.327
- Water bridges: B:R.174, B:N.329
- pi-Cation interactions: B:R.174, B:F.327
R9V.25: 4 residues within 4Å:- Chain B: Y.456
- Chain C: R.174, F.327, N.329
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:R.174, C:F.327, C:F.327, C:F.327
- Water bridges: C:R.174, C:N.329
- pi-Cation interactions: C:R.174, C:F.327
R9V.34: 3 residues within 4Å:- Chain D: P.451, K.452, E.455
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:E.455
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 5 residues within 4Å:- Chain A: T.170, H.173, G.302
- Chain D: Y.456
- Ligands: R9V.4
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain A- Water bridges: D:Y.456, D:Y.456, A:T.169, A:G.302
- Hydrogen bonds: A:H.173
GOL.12: 8 residues within 4Å:- Chain A: D.219, K.346
- Chain B: W.26, E.30, Q.94, Q.96, R.216, T.383
9 PLIP interactions:5 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:E.30, B:Q.94, B:Q.96, B:R.216, A:K.346, A:K.346
- Water bridges: B:D.95, A:D.219, A:D.219
GOL.15: 5 residues within 4Å:- Chain B: K.429, S.460, E.462, G.463, P.464
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.460, B:S.460, B:E.462
GOL.16: 6 residues within 4Å:- Chain B: A.24, A.25, R.28, A.100, A.103, A.104
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.24, B:R.28, B:A.100
GOL.33: 8 residues within 4Å:- Chain C: D.219, K.346
- Chain D: W.26, E.30, Q.94, Q.96, R.216, T.383
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:E.30, D:Q.94, D:Q.96, D:R.216, C:K.346
- 4 x K: POTASSIUM ION(Non-covalent)
K.7: 5 residues within 4Å:- Chain A: Q.68, T.383, G.384, H.385, P.386
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.383, A:T.383, A:H.385, H2O.4, H2O.8
K.18: 5 residues within 4Å:- Chain B: Q.68, T.383, G.384, H.385, P.386
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.383, B:T.383, B:H.385, H2O.8, H2O.21
K.26: 4 residues within 4Å:- Chain C: Q.68, T.383, G.384, H.385
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:T.383, C:T.383, C:H.385, H2O.37, H2O.39
K.35: 6 residues within 4Å:- Chain D: Q.68, T.383, G.384, H.385, P.386
- Ligands: ADE.32
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:T.383, D:T.383, D:H.385, H2O.49, H2O.51
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.8: 6 residues within 4Å:- Chain A: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.9: 5 residues within 4Å:- Chain A: R.28, I.32, E.35, E.74
- Chain B: H.363
Ligand excluded by PLIPPO4.10: 10 residues within 4Å:- Chain A: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.1, ADE.2
Ligand excluded by PLIPPO4.11: 5 residues within 4Å:- Chain A: G.458, V.459, P.464, K.466, P.467
Ligand excluded by PLIPPO4.19: 6 residues within 4Å:- Chain B: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.20: 10 residues within 4Å:- Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.13, ADE.14
Ligand excluded by PLIPPO4.21: 5 residues within 4Å:- Chain B: G.458, V.459, P.464, K.466, P.467
Ligand excluded by PLIPPO4.22: 5 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35, E.74
Ligand excluded by PLIPPO4.27: 6 residues within 4Å:- Chain C: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.28: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.23, ADE.24
Ligand excluded by PLIPPO4.29: 6 residues within 4Å:- Chain C: G.458, V.459, P.464, F.465, K.466, P.467
Ligand excluded by PLIPPO4.30: 5 residues within 4Å:- Chain C: R.28, I.32, E.35, E.74
- Chain D: H.363
Ligand excluded by PLIPPO4.36: 6 residues within 4Å:- Chain D: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.37: 10 residues within 4Å:- Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.31, ADE.32
Ligand excluded by PLIPPO4.38: 6 residues within 4Å:- Chain D: G.458, V.459, P.464, F.465, K.466, P.467
Ligand excluded by PLIPPO4.39: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Malecki, P.H. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry E06. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 5 x R9V: (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 4 x K: POTASSIUM ION(Non-covalent)
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Malecki, P.H. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry E06. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D