- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.13 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: I.63, 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
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.68, A:T.69, A:H.385
- Water bridges: A:H.64, A:D.142
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, PO4.17
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.68, B:H.385
ADE.21: 13 residues within 4Å:- Chain C: I.63, H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.20, PO4.25
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:T.66, C:Q.68, C:H.385
ADE.34: 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.33, K.36, PO4.39
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:T.66, D:Q.68, D:T.69, 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.3, H2O.15
K.15: 4 residues within 4Å:- Chain B: Q.68, T.383, G.384, H.385
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.383, B:T.383, B:H.385, H2O.15, H2O.17
K.23: 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.25, H2O.25
K.36: 5 residues within 4Å:- Chain D: Q.68, T.383, G.384, H.385
- Ligands: ADE.34
5 PLIP interactions:2 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:T.383, D:T.383, H2O.25, H2O.35, H2O.36
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.4: 5 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35, E.74
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:E.35, B:E.35
- Water bridges: B:R.28, B:R.45, B:R.45
- Salt bridges: B:R.28, A:H.363
PO4.5: 5 residues within 4Å:- Chain A: K.313, A.314, L.315, K.317, R.354
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.317
- Water bridges: A:R.354, A:R.354
- Salt bridges: A:R.354
PO4.6: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Salt bridges: A:R.28, B:H.363
PO4.7: 9 residues within 4Å:- Chain A: D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.1, ADE.2
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.64, A:D.201, A:D.201
- Salt bridges: A:K.197
PO4.16: 5 residues within 4Å:- Chain B: K.313, 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
PO4.17: 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
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.167, B:T.168, B:H.385
- Salt bridges: B:K.197
PO4.24: 5 residues within 4Å:- Chain C: R.28, I.32, E.35, E.74
- Chain D: H.363
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:E.35, C:E.74
- Water bridges: C:R.45
- Salt bridges: C:R.28, D:H.363
PO4.25: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.20, ADE.21
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:H.64, C:E.167, C:T.168, C:D.201
- Water bridges: C:D.142
- Salt bridges: C:K.197
PO4.26: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)PO4.27: 4 residues within 4Å:- Chain C: G.458, P.464, K.466, P.467
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:P.464
- Water bridges: C:D.468
PO4.28: 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
PO4.37: 5 residues within 4Å:- Chain D: K.313, A.314, L.315, K.317, R.354
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:K.317
- Water bridges: D:K.313, D:R.354, D:R.354, D:D.366
- Salt bridges: D:R.354
PO4.38: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Water bridges: D:E.35, D:R.45
- Salt bridges: D:R.28, C:H.363
PO4.39: 10 residues within 4Å:- Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.33, ADE.34
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
PO4.40: 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, D:P.464
- 14 x RB7: N-[(4-bromo-3-methylphenyl)methyl]-2-(methylsulfonyl)ethan-1-amine(Non-covalent)
RB7.8: 9 residues within 4Å:- Chain A: A.40, G.43, L.44, K.47, Y.48, L.430, E.433, V.434, E.437
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:L.44, A:K.47, A:V.434
- Hydrogen bonds: A:K.47, A:Y.48, A:E.433
RB7.9: 7 residues within 4Å:- Chain A: I.189, H.403, V.425, L.426, P.427, K.429, L.430
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:I.189, A:P.427, A:L.430
- pi-Stacking: A:H.403
RB7.10: 10 residues within 4Å:- Chain A: E.116, Y.119, E.120, D.145, E.148, I.149, R.174, F.327
- Chain D: Y.456
- Ligands: RB7.11
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Y.119, A:Y.119, A:I.149
- Hydrogen bonds: A:D.145
RB7.11: 6 residues within 4Å:- Chain A: E.116, E.117, E.120, E.148, I.149
- Ligands: RB7.10
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.120
RB7.12: 5 residues within 4Å:- Chain A: K.17, V.18, W.111, E.118, W.121
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:E.118
- Hydrogen bonds: A:E.118
- pi-Stacking: A:W.121, A:W.121
RB7.18: 10 residues within 4Å:- Chain B: E.116, Y.119, E.120, D.145, E.148, I.149, R.174, F.327
- Chain C: Y.456
- Ligands: RB7.19
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:Y.119, B:Y.119, B:I.149
- Hydrogen bonds: B:D.145, B:R.174
RB7.19: 5 residues within 4Å:- Chain B: E.120, E.148, I.149, K.152
- Ligands: RB7.18
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:E.148
- Hydrogen bonds: B:E.120
RB7.29: 9 residues within 4Å:- Chain C: A.40, G.43, L.44, K.47, Y.48, L.430, E.433, V.434, E.437
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:K.47, C:E.433
- Hydrogen bonds: C:K.47, C:E.433
RB7.30: 9 residues within 4Å:- Chain C: I.189, H.403, K.419, R.420, E.424, V.425, L.426, P.427, L.430
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.189, C:P.427
- pi-Cation interactions: C:H.403
RB7.31: 5 residues within 4Å:- Chain C: E.120, I.149, K.152, K.153
- Ligands: RB7.32
No protein-ligand interaction detected (PLIP)RB7.32: 10 residues within 4Å:- Chain B: Y.456
- Chain C: E.116, Y.119, E.120, D.145, E.148, I.149, R.174, F.327
- Ligands: RB7.31
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:Y.119, C:Y.119
- Hydrogen bonds: C:D.145, C:R.174, C:R.174
RB7.41: 9 residues within 4Å:- Chain A: Y.456
- Chain D: Y.119, E.120, D.145, E.148, I.149, R.174, F.327
- Ligands: RB7.43
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:Y.119, D:I.149
- Water bridges: D:D.145, D:D.145
RB7.42: 10 residues within 4Å:- Chain D: Y.48, I.189, L.399, I.402, H.403, E.424, V.425, L.426, P.427, L.430
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:I.189, D:H.403, D:E.424, D:L.426, D:P.427, D:L.430
- Hydrogen bonds: D:H.403
- pi-Stacking: D:H.403
RB7.43: 4 residues within 4Å:- Chain D: E.120, E.148, I.149
- Ligands: RB7.41
No protein-ligand interaction detected (PLIP)- 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 F04. 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 2.13 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)
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
- 14 x RB7: N-[(4-bromo-3-methylphenyl)methyl]-2-(methylsulfonyl)ethan-1-amine(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 F04. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D