- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 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, PO4.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.68, A:T.69, A:H.385
ADE.10: 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.9, PO4.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.68, B:H.385
ADE.15: 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.14, PO4.19
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:T.66, C:Q.68, C:H.385
ADE.25: 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.24, PO4.32
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385
- 3 x SZ7: ~{N}-[(~{E})-thiophen-2-ylmethylideneamino]cyclopropanecarboxamide(Non-covalent)
SZ7.3: 7 residues within 4Å:- Chain A: Y.48, L.399, I.402, H.403, E.406, Q.407, L.430
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:L.399, A:I.402, A:Q.407, A:L.430
- Hydrogen bonds: A:E.406, A:E.406
SZ7.23: 7 residues within 4Å:- Chain C: Y.48, L.399, I.402, H.403, E.406, Q.407, L.430
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:L.399, C:I.402, C:L.430
- Hydrogen bonds: C:E.406
SZ7.27: 7 residues within 4Å:- Chain D: Y.48, L.399, I.402, H.403, E.406, Q.407, L.430
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:L.399, D:I.402, D:L.430
- Hydrogen bonds: D:H.403, D:E.406
- 4 x K: POTASSIUM ION(Non-covalent)
K.4: 4 residues within 4Å:- Chain A: Q.68, T.383, G.384, H.385
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.383, A:T.383, A:H.385, H2O.8, H2O.10
K.11: 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.9, H2O.28
K.17: 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.39, H2O.40
K.29: 5 residues within 4Å:- Chain D: Q.68, T.383, G.384, H.385, P.386
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:T.383, D:T.383, D:H.385, H2O.58, H2O.60
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.5: 4 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:E.35, B:E.35
- Water bridges: B:R.45, B:R.45
- Salt bridges: B:R.28, A:H.363
PO4.6: 6 residues within 4Å:- Chain A: K.313, A.314, L.315, K.316, K.317, R.354
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.317
- Water bridges: A:R.354, A:D.366
- Salt bridges: A:R.354
PO4.7: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Water bridges: A:R.45, A:E.74
- Salt bridges: A:R.28, B:H.363
PO4.8: 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
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:H.64, A:D.201, A:D.201
- Water bridges: A:T.168
- Salt bridges: A:K.197
PO4.12: 6 residues within 4Å:- Chain B: K.313, A.314, L.315, K.316, K.317, R.354
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:A.314, B:L.315, B:K.317
- Salt bridges: B:R.354
PO4.13: 10 residues within 4Å:- Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.9, ADE.10
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.167, B:T.168
- Water bridges: B:T.168, B:T.168
- Salt bridges: B:K.197
PO4.18: 4 residues within 4Å:- Chain C: R.28, I.32, E.35
- Chain D: H.363
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:E.35
- Water bridges: C:R.45, C:R.45, D:H.363
- Salt bridges: C:R.28, D:H.363
PO4.19: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.14, ADE.15
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:H.64, C:E.167, C:T.168, C:D.201
- Water bridges: C:D.142, C:T.168
- Salt bridges: C:K.197
PO4.20: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)PO4.21: 6 residues within 4Å:- Chain C: G.458, V.459, P.464, F.465, K.466, P.467
2 PLIP interactions:2 interactions with chain C- Water bridges: C:I.457, C:G.458
PO4.22: 6 residues within 4Å:- Chain C: K.313, A.314, L.315, K.316, K.317, R.354
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:L.315, C:L.315, C:K.317
- Salt bridges: C:R.354
PO4.30: 6 residues within 4Å:- Chain D: K.313, A.314, L.315, K.316, K.317, R.354
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:K.317
- Water bridges: D:R.354, D:R.354, D:D.366
- Salt bridges: D:R.354
PO4.31: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain C- Water bridges: D:R.45, D:R.45, D:R.45
- Salt bridges: D:R.28, C:H.363
PO4.32: 10 residues within 4Å:- Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.24, ADE.25
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:H.64, D:T.168, D:D.201, D:D.201
- Salt bridges: D:K.197
PO4.33: 6 residues within 4Å:- Chain D: G.458, V.459, P.464, F.465, K.466, P.467
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:G.458
- Water bridges: D:G.458
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.16: 8 residues within 4Å:- Chain B: D.468, T.469, Y.470, R.471
- Chain C: D.468, T.469, Y.470, R.471
No protein-ligand interaction detected (PLIP)DMS.26: 8 residues within 4Å:- Chain A: D.468, T.469, Y.470, R.471
- Chain D: D.468, T.469, Y.470, R.471
1 PLIP interactions:1 interactions with chain D- Water bridges: D:Y.470
DMS.28: 3 residues within 4Å:- Chain D: A.418, K.419, L.421
No protein-ligand interaction detected (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 G12. 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 1.72 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
- 3 x SZ7: ~{N}-[(~{E})-thiophen-2-ylmethylideneamino]cyclopropanecarboxamide(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
- 3 x DMS: DIMETHYL SULFOXIDE(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 G12. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D