- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.61 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
ADE.2: 13 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, K.6, PO4.9
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385
ADE.13: 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.12, PO4.20
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.385
- Water bridges: B:H.64, B:D.142
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: 12 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, 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 UI4: 4-pyridin-2-ylphenol(Non-covalent)
UI4.4: 7 residues within 4Å:- Chain A: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:H.403, A:L.426, A:L.430
- pi-Stacking: A:H.403
UI4.5: 12 residues within 4Å:- Chain A: K.203, Y.204, R.207, Y.232, K.237, Q.241, Q.262, D.266
- Chain D: K.203, Y.204, D.266, Y.472
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain D- Hydrophobic interactions: A:K.203, A:Y.204, A:K.237, A:Q.241
- Water bridges: D:D.266
UI4.16: 7 residues within 4Å:- Chain B: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:L.399, B:I.402, B:H.403, B:L.426, B:P.427, B:L.430
- pi-Stacking: B:H.403
UI4.25: 9 residues within 4Å:- Chain C: Y.48, Q.51, P.53, L.399, I.402, H.403, E.406, P.427, L.430
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:Y.48, C:P.53, C:I.402, C:H.403, C:L.430
- Water bridges: C:E.406
UI4.34: 7 residues within 4Å:- Chain D: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
7 PLIP interactions:7 interactions with chain D- Hydrophobic interactions: D:L.399, D:I.402, D:H.403, D:L.426, D:P.427, D:L.430
- pi-Stacking: D:H.403
- 4 x K: POTASSIUM ION(Non-covalent)
K.6: 6 residues within 4Å:- Chain A: Q.68, T.383, G.384, H.385, P.386
- Ligands: ADE.2
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.10
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.22, H2O.25
K.26: 5 residues within 4Å:- Chain C: Q.68, T.383, G.384, H.385, P.386
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:T.383, C:T.383, C:H.385, H2O.38, H2O.38
K.35: 4 residues within 4Å:- Chain D: Q.68, T.383, G.384, H.385
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:T.383, D:T.383, D:H.385, H2O.55, H2O.59
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 7 residues within 4Å:- Chain A: K.313, A.314, L.315, K.316, K.317, R.354, D.366
Ligand excluded by PLIPPO4.8: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
Ligand excluded by PLIPPO4.9: 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 PLIPPO4.10: 6 residues within 4Å:- Chain A: G.458, V.459, P.464, F.465, 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.12, ADE.13
Ligand excluded by PLIPPO4.21: 6 residues within 4Å:- Chain B: G.458, V.459, P.464, F.465, K.466, P.467
Ligand excluded by PLIPPO4.22: 4 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35
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: 4 residues within 4Å:- Chain C: R.28, I.32, E.35
- 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- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 8 residues within 4Å:- Chain A: D.219, K.346
- Chain B: W.26, E.30, Q.94, Q.96, R.216, T.383
8 PLIP interactions:4 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:K.346, A:K.346, B:E.30, B:Q.94, B:Q.96, B:R.216
- Water bridges: A:D.219, A:D.219
GOL.14: 4 residues within 4Å:- Chain B: S.460, E.462, G.463, P.464
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.460, B:S.460
GOL.15: 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.17: 4 residues within 4Å:- Chain B: V.459, S.460, V.461, E.462
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:V.461, B:E.462
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
6 PLIP interactions:5 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
- Water bridges: D:D.95
- 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 F09. 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 1.61 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 UI4: 4-pyridin-2-ylphenol(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
- 5 x GOL: GLYCEROL(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 F09. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D