- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 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
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385
ADE.12: 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.11, PO4.18
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.385
ADE.22: 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.21, PO4.25
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.68, C:T.69, C:H.385
ADE.29: 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.28, PO4.35
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.68, D:H.385
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 2 x REG: 1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea(Non-covalent)
REG.4: 8 residues within 4Å:- Chain A: L.44, K.47, Y.48, L.399, L.430, E.433, V.434, E.437
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:L.44, A:V.434, A:E.437
- Hydrogen bonds: A:K.47, A:E.433, A:E.433, A:E.433
REG.31: 8 residues within 4Å:- Chain D: L.44, K.47, Y.48, L.399, L.430, E.433, V.434, E.437
7 PLIP interactions:7 interactions with chain D- Hydrophobic interactions: D:K.47, D:E.433, D:V.434, D:E.437
- Hydrogen bonds: D:K.47, D:E.433, D:E.433
- 4 x K: POTASSIUM ION(Non-covalent)
K.5: 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.4, H2O.9
K.16: 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.22, H2O.23
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.37, H2O.37
K.33: 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.51, H2O.52
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 6 residues within 4Å:- Chain A: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.7: 4 residues within 4Å:- Chain A: R.28, I.32, E.35
- Chain B: H.363
Ligand excluded by PLIPPO4.8: 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
Ligand excluded by PLIPPO4.9: 5 residues within 4Å:- Chain A: G.458, V.459, P.464, K.466, P.467
Ligand excluded by PLIPPO4.17: 6 residues within 4Å:- Chain B: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.18: 10 residues within 4Å:- Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.11, ADE.12
Ligand excluded by PLIPPO4.19: 5 residues within 4Å:- Chain B: G.458, V.459, P.464, K.466, P.467
Ligand excluded by PLIPPO4.20: 4 residues within 4Å:- Chain A: H.363
- Chain B: R.28, I.32, E.35
Ligand excluded by PLIPPO4.24: 6 residues within 4Å:- Chain C: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.25: 10 residues within 4Å:- Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.21, ADE.22
Ligand excluded by PLIPPO4.26: 6 residues within 4Å:- Chain C: G.458, V.459, P.464, F.465, K.466, P.467
Ligand excluded by PLIPPO4.27: 4 residues within 4Å:- Chain C: R.28, I.32, E.35
- Chain D: H.363
Ligand excluded by PLIPPO4.34: 6 residues within 4Å:- Chain D: K.313, A.314, L.315, K.316, K.317, R.354
Ligand excluded by PLIPPO4.35: 10 residues within 4Å:- Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390
- Ligands: NAD.28, ADE.29
Ligand excluded by PLIPPO4.36: 6 residues within 4Å:- Chain D: G.458, V.459, P.464, F.465, K.466, P.467
Ligand excluded by PLIPPO4.37: 4 residues within 4Å:- Chain C: H.363
- Chain D: R.28, I.32, E.35
Ligand excluded by PLIP- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.10: 7 residues within 4Å:- Chain A: D.219, K.346
- Chain B: W.26, E.30, Q.94, Q.96, T.383
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:E.30, B:Q.94, B:Q.96, B:R.216, A:K.346, A:K.346
- Water bridges: A:D.219
GOL.13: 5 residues within 4Å:- Chain B: S.460, E.462, G.463, P.464
- Ligands: GOL.15
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.460, B:S.460
GOL.14: 6 residues within 4Å:- Chain B: A.24, A.25, R.28, A.100, A.103, A.104
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.24, B:R.28, B:A.100
GOL.15: 4 residues within 4Å:- Chain B: S.460, V.461, E.462
- Ligands: GOL.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:V.461, B:E.462
GOL.30: 7 residues within 4Å:- Chain C: D.219, K.346
- Chain D: W.26, E.30, Q.94, Q.96, T.383
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:E.30, D:Q.94, D:Q.96, C:K.346
- Water bridges: D:D.95, D:R.216
GOL.32: 6 residues within 4Å:- Chain A: K.203, Y.204
- Chain D: K.203, K.237, Q.262, D.266
7 PLIP interactions:4 interactions with chain D, 3 interactions with chain A- Hydrogen bonds: D:Q.262, A:K.203, A:Y.204
- Water bridges: D:K.203, D:K.203, D:K.237, A:Y.204
- 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 H11. 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 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 4 x ADE: ADENINE(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 2 x REG: 1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 16 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 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 H11. To be published
- Release Date
- 2024-02-21
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D