- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.37 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
K.2: 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.8, H2O.9
K.9: 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.28, H2O.28
K.23: 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.47, H2O.48
K.30: 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.67, H2O.67
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Water bridges: A:E.35, A:R.45, A:R.45, A:R.45
- Salt bridges: A:R.28, B: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- Water bridges: A:K.317, A:K.317
- Salt bridges: A:K.317, A:R.354
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.5
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.64, A:T.168
- Salt bridges: A:K.197
PO4.10: 4 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35
8 PLIP interactions:6 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:E.35, B:E.35
- Water bridges: B:R.45, B:R.45, B:R.45, A:H.363
- Salt bridges: B:R.28, A:H.363
PO4.20: 10 residues within 4Å:- Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.8, ADE.19
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:D.142, B:E.167, B:E.167, B:T.168
- Water bridges: B:D.142, B:T.168
- Salt bridges: B:K.197
PO4.21: 6 residues within 4Å:- Chain B: K.203, Y.204
- Chain C: K.203, K.237, Q.262, D.266
7 PLIP interactions:3 interactions with chain C, 4 interactions with chain B- Hydrogen bonds: C:Q.262
- Water bridges: C:D.266, B:K.203, B:K.203, B:Y.472
- Salt bridges: C:K.203, B:K.203
PO4.24: 4 residues within 4Å:- Chain C: R.28, I.32, E.35
- Chain D: H.363
7 PLIP interactions:6 interactions with chain C, 1 interactions with chain D- Water bridges: C:E.35, C:E.35, C:R.45, C:R.45, C:R.45
- Salt bridges: C:R.28, D:H.363
PO4.27: 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- Water bridges: C:K.317, C:K.317
- Salt bridges: C:K.317, C:R.354
PO4.28: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.22, ADE.26
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:H.64, C:E.167, C:T.168, C:T.168
- Salt bridges: C:K.197
PO4.31: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
8 PLIP interactions:6 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:E.35, D:E.35
- Water bridges: D:R.45, D:R.45, D:R.45, C:H.363
- Salt bridges: D:R.28, C:H.363
PO4.41: 10 residues within 4Å:- Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.29, ADE.40
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:D.142, D:E.167
- Water bridges: D:D.142, D:T.168
- Salt bridges: D:K.197
PO4.42: 6 residues within 4Å:- Chain A: K.203, K.237, Q.262, D.266
- Chain D: K.203, Y.204
7 PLIP interactions:2 interactions with chain A, 5 interactions with chain D- Hydrogen bonds: A:Q.262, D:Y.204
- Salt bridges: A:K.203, D:K.203
- Water bridges: D:K.203, D:K.203, D:K.203
- 4 x UIS: N-[3-(diethylamino)phenyl]ethanamide(Non-covalent)
UIS.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:I.402, A:H.403, A:L.426, A:L.430
UIS.17: 7 residues within 4Å:- Chain B: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:I.402, B:H.403, B:L.426, B:L.430
UIS.25: 7 residues within 4Å:- Chain C: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:I.402, C:H.403, C:L.426, C:L.430
UIS.38: 7 residues within 4Å:- Chain D: Y.48, L.399, I.402, H.403, L.426, P.427, L.430
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:I.402, D:H.403, D:L.426, D:L.430
- 4 x ADE: ADENINE(Non-covalent)
ADE.5: 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.19: 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.8, PO4.20
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.68, B:H.385
ADE.26: 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.22, PO4.28
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Q.68, C:H.385
ADE.40: 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.29, PO4.41
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385
- 10 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.11: 5 residues within 4Å:- Chain B: K.313, A.314, L.315, K.317, R.354
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.354
- Salt bridges: B:D.366
DMS.13: 4 residues within 4Å:- Chain B: K.58, E.82, W.134, D.135
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:E.82, B:D.135
DMS.14: 5 residues within 4Å:- Chain B: G.458, V.459, P.464, K.466, P.467
No protein-ligand interaction detected (PLIP)DMS.15: 3 residues within 4Å:- Chain B: K.17, V.18, W.111
2 PLIP interactions:2 interactions with chain B- pi-Cation interactions: B:W.111, B:W.111
DMS.18: 2 residues within 4Å:- Chain B: R.337, W.342
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.337
- pi-Cation interactions: B:W.342
DMS.32: 5 residues within 4Å:- Chain D: K.313, A.314, L.315, K.317, R.354
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:R.354
- Salt bridges: D:D.366
DMS.34: 4 residues within 4Å:- Chain D: K.58, E.82, W.134, D.135
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:E.82, D:D.135
DMS.35: 5 residues within 4Å:- Chain D: G.458, V.459, P.464, K.466, P.467
No protein-ligand interaction detected (PLIP)DMS.36: 3 residues within 4Å:- Chain D: K.17, V.18, W.111
2 PLIP interactions:2 interactions with chain D- pi-Cation interactions: D:W.111, D:W.111
DMS.39: 2 residues within 4Å:- Chain D: R.337, W.342
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:R.337
- pi-Cation interactions: D:W.342
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 4 residues within 4Å:- Chain B: K.112, G.113, P.347, Q.348
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.348
GOL.16: 2 residues within 4Å:- Chain B: D.361, H.363
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.361, B:H.363
GOL.33: 4 residues within 4Å:- Chain D: K.112, G.113, P.347, Q.348
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Q.348
GOL.37: 2 residues within 4Å:- Chain D: D.361, H.363
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.361, D:H.363, D:H.363
- 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 B07. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
AD
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.37 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x UIS: N-[3-(diethylamino)phenyl]ethanamide(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
- 10 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 4 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 B07. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
AD
C