- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.02 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, PO4.7
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385
ADE.9: 13 residues within 4Å:- Chain B: I.63, H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.8, PO4.15
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.385
ADE.17: 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.16, PO4.22
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Q.68, C:H.385
ADE.25: 13 residues within 4Å:- Chain D: I.63, H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.24, PO4.28
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.68, D:H.385
- 4 x K: POTASSIUM ION(Non-covalent)
K.3: 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.6, H2O.6
K.12: 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.16, H2O.18
K.19: 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.28, H2O.30
K.26: 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.42, H2O.43
- 14 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.4: 6 residues within 4Å:- Chain A: G.458, V.459, P.464, F.465, K.466, P.467
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.466
PO4.5: 6 residues within 4Å:- Chain A: K.313, A.314, L.315, K.316, K.317, R.354
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.314, A:K.317
- Salt bridges: A:R.354
PO4.6: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
7 PLIP interactions:1 interactions with chain B, 6 interactions with chain A- Salt bridges: B:H.363, A:R.28
- Hydrogen bonds: A:E.35, A:E.35
- Water bridges: A:R.45, A:R.45, A:R.45
PO4.7: 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
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:T.168, A:D.201, A:D.201
- Water bridges: A:H.64, A:D.142
- Salt bridges: A:K.197
PO4.13: 5 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35, E.74
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
PO4.14: 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:L.315, B:L.315, B:K.317
- Salt bridges: B:R.354
PO4.15: 10 residues within 4Å:- Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.8, ADE.9
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.168, B:D.201, B:D.201
- Salt bridges: B:K.197
PO4.20: 4 residues within 4Å:- Chain C: R.28, I.32, E.35
- Chain D: H.363
6 PLIP interactions:1 interactions with chain D, 5 interactions with chain C- Salt bridges: D:H.363, C:R.28
- Water bridges: C:R.45, C:R.45, C:R.45, C:R.45
PO4.21: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Water bridges: D:R.45
- Salt bridges: D:R.28, C:H.363
PO4.22: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.16, ADE.17
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:E.167, C:T.168
- Water bridges: C:T.168, C:T.168
- Salt bridges: C:K.197
PO4.23: 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- Hydrogen bonds: C:K.466
- Water bridges: C:D.468
PO4.27: 6 residues within 4Å:- Chain D: K.313, A.314, L.315, K.316, K.317, R.354
7 PLIP interactions:7 interactions with chain D- Water bridges: D:K.313, D:K.317, D:K.317, D:R.354, D:R.354, D:D.366
- Salt bridges: D:R.354
PO4.28: 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
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.167
- Salt bridges: D:K.197
PO4.29: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 1 x SZA: ~{N}-(2-thiophen-2-ylethyl)pyridine-4-carboxamide(Non-covalent)
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.11: 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.18: 5 residues within 4Å:- Chain C: K.313, A.314, L.315, K.317, R.354
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.354, C:R.354
- Salt bridges: C:D.366
- 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 H12. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.02 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 14 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x SZA: ~{N}-(2-thiophen-2-ylethyl)pyridine-4-carboxamide(Non-covalent)
- 2 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 H12. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
J