- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADN: ADENOSINE(Non-covalent)
ADN.2: 20 residues within 4Å:- Chain A: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.1, K.7, ZN.8
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:T.168, A:K.197, A:K.197, A:H.385
ADN.13: 20 residues within 4Å:- Chain B: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.12, K.16, ZN.17
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:Q.68, B:T.69, B:E.167, B:T.168, B:T.168, B:K.197, B:K.197, B:H.326, B:H.385
ADN.24: 19 residues within 4Å:- Chain C: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.23, ZN.30
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:T.66, C:Q.68, C:T.168, C:K.197, C:K.197, C:H.385
ADN.34: 20 residues within 4Å:- Chain D: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, L.379, T.383, G.384, H.385, M.390, F.394
- Ligands: NAD.33, K.35, ZN.36
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:Q.68, D:T.69, D:E.167, D:T.168, D:T.168, D:K.197, D:K.197, D:H.385
- 5 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)
BU1.3: 4 residues within 4Å:- Chain A: K.17, V.18, W.111, E.118
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.17
- Water bridges: A:V.18
BU1.4: 4 residues within 4Å:- Chain A: F.13, Y.16, A.102, A.103
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.13
- Hydrogen bonds: A:Y.16
BU1.6: 4 residues within 4Å:- Chain A: E.148, H.151, K.152, M.178
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:E.148
- Hydrogen bonds: A:K.152
- Water bridges: A:K.152
BU1.14: 5 residues within 4Å:- Chain B: K.17, V.18, W.111, E.118
- Ligands: BU1.15
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.118
- Water bridges: B:K.17, B:K.17, B:K.17
BU1.15: 4 residues within 4Å:- Chain B: T.14, Y.16, K.17
- Ligands: BU1.14
No protein-ligand interaction detected (PLIP)- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 4 x K: POTASSIUM ION(Non-covalent)
K.7: 6 residues within 4Å:- Chain A: Q.68, T.383, G.384, H.385, P.386
- Ligands: ADN.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.6, H2O.8
K.16: 5 residues within 4Å:- Chain B: Q.68, T.383, G.384, H.385
- Ligands: ADN.13
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.383, B:T.383, B:H.385, H2O.23, H2O.25
K.29: 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.43, H2O.46
K.35: 6 residues within 4Å:- Chain D: Q.68, T.383, G.384, H.385, P.386
- Ligands: ADN.34
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:T.383, D:T.383, D:H.385, H2O.62, H2O.65
- 16 x ZN: ZINC ION(Non-covalent)
ZN.8: 6 residues within 4Å:- Chain A: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.2
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:C.88, A:D.142, A:D.142, A:H.326
ZN.9: 2 residues within 4Å:- Chain A: H.403, E.424
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:H.403, A:E.424, H2O.2, H2O.7, H2O.13
ZN.10: 3 residues within 4Å:- Chain A: H.173, D.177
- Chain D: Y.456
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:H.173, A:D.177, H2O.2, H2O.15, H2O.16
ZN.11: 2 residues within 4Å:- Chain A: H.173
- Ligands: PG4.5
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.173, H2O.15, H2O.18
ZN.17: 6 residues within 4Å:- Chain B: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.13
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.88, B:D.142, B:D.142, B:H.326
ZN.18: 2 residues within 4Å:- Chain B: H.403, E.424
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:H.403, B:E.424, H2O.21, H2O.34, H2O.34
ZN.19: 3 residues within 4Å:- Chain B: H.173, D.177
- Chain C: Y.456
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:H.173, B:D.177, H2O.21, H2O.34, H2O.54
ZN.20: 1 residues within 4Å:- Chain B: H.363
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:H.363, H2O.17, H2O.36, H2O.37
ZN.30: 6 residues within 4Å:- Chain C: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.24
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:C.88, C:D.142, C:D.142, C:H.326
ZN.31: 2 residues within 4Å:- Chain C: H.403, E.424
5 PLIP interactions:2 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:H.403, C:E.424, H2O.40, H2O.52, H2O.56
ZN.32: 3 residues within 4Å:- Chain B: Y.456
- Chain C: H.173, D.177
5 PLIP interactions:2 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:H.173, C:D.177, H2O.48, H2O.51, H2O.54
ZN.36: 6 residues within 4Å:- Chain D: H.64, C.88, D.142, G.143, H.326
- Ligands: ADN.34
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.88, D:D.142, D:D.142, D:H.326
ZN.37: 3 residues within 4Å:- Chain D: H.403, Q.407, E.424
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:H.403, D:E.424, H2O.61, H2O.70
ZN.38: 3 residues within 4Å:- Chain A: Y.456
- Chain D: H.173, D.177
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:H.173, D:D.177, H2O.14
ZN.39: 1 residues within 4Å:- Chain D: H.173
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:H.173, H2O.67, H2O.68
ZN.40: 2 residues within 4Å:- Chain D: D.361, H.363
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.361, D:D.361, D:H.363
- 1 x BCN: BICINE(Non-covalent)
- 2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
HEZ.22: 7 residues within 4Å:- Chain B: I.457, G.458, V.459, P.464, K.466, P.467
- Chain C: H.173
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.459
HEZ.27: 4 residues within 4Å:- Chain C: E.148, H.151, K.152, M.178
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:E.148, C:H.151, C:K.152
- Hydrogen bonds: C:K.152
- 3 x PDO: 1,3-PROPANDIOL(Non-covalent)
PDO.25: 4 residues within 4Å:- Chain C: K.17, V.18, W.111, E.118
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:V.18, C:E.118
- Water bridges: C:K.17, C:K.17, C:K.17
PDO.26: 2 residues within 4Å:- Chain C: T.14, Y.16
No protein-ligand interaction detected (PLIP)PDO.28: 4 residues within 4Å:- Chain C: W.26, R.29
- Chain D: K.346, P.347
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.29
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Malecki, P.H. et al., Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions. To Be Published
- Release Date
- 2023-04-19
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADN: ADENOSINE(Non-covalent)
- 5 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 4 x K: POTASSIUM ION(Non-covalent)
- 16 x ZN: ZINC ION(Non-covalent)
- 1 x BCN: BICINE(Non-covalent)
- 2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
- 3 x PDO: 1,3-PROPANDIOL(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Malecki, P.H. et al., Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions. To Be Published
- Release Date
- 2023-04-19
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D