SMTL ID : 8ajt.1

Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 18 residues within 4Å: Chain A: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.2, K.6 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.9: 18 residues within 4Å: Chain B: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.10, K.13 10 PLIP interactions: 10 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.385 Water bridges: B:D.142, B:D.142 ADN.18: 18 residues within 4Å: Chain C: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.17, K.24 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.27: 18 residues within 4Å: Chain D: H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.28, K.32 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

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 31 residues within 4Å: Chain A: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, A.326, L.376, N.378, H.385 Chain D: Q.453, K.466, Y.470 Ligands: ADN.1, TRS.3 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:N.202, A:V.235 Hydrogen bonds: A:T.169, A:T.169, A:T.169, A:T.170, A:T.170, A:N.202, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:A.326, A:N.378, A:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466, D:Y.470 Water bridges: A:G.233, A:D.234, A:D.234, A:G.236, A:F.327, A:E.330 NAD.10: 32 residues within 4Å: Chain B: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, A.326, L.376, N.378, H.385 Chain C: L.449, Q.453, K.466, Y.470 Ligands: ADN.9, TRS.11 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.169, B:T.170, B:T.170, B:T.170, B:N.202, B:D.234, B:V.235, B:V.255, B:D.256, B:N.303, B:N.378, B:N.378, C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470, C:Y.470 Water bridges: B:G.233, B:D.234, B:D.234, B:G.236 NAD.17: 31 residues within 4Å: Chain B: Q.453, K.466, Y.470 Chain C: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, A.326, L.376, N.378, H.385 Ligands: ADN.18, TRS.19 26 PLIP interactions: 21 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:N.202, C:V.235 Hydrogen bonds: C:T.169, C:T.169, C:T.169, C:T.170, C:N.202, C:D.234, C:V.235, C:V.255, C:D.256, C:N.303, C:A.326, C:N.378, C:N.378, B:Q.453, B:Q.453, B:K.466, B:K.466, B:Y.470 Water bridges: C:G.233, C:D.234, C:D.234, C:G.236, C:F.327, C:E.330 NAD.28: 31 residues within 4Å: Chain A: Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, A.326, L.376, N.378, H.385 Ligands: ADN.27, TRS.29 27 PLIP interactions: 6 interactions with chain A, 21 interactions with chain D Hydrogen bonds: A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470, D:T.169, D:T.169, D:T.169, D:T.170, D:T.170, D:N.202, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:A.326, D:N.378, D:N.378 Hydrophobic interactions: D:N.202, D:V.235 Water bridges: D:N.192, D:G.233, D:G.236, D:F.327, D:E.330

8 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: T.169, T.170, H.173, T.301, G.302 Chain D: I.457 Ligands: NAD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.169, A:H.173, A:T.301 Water bridges: A:G.302 TRS.4: 5 residues within 4Å: Chain A: A.40, G.43, L.44, K.47, E.437 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.40 TRS.11: 7 residues within 4Å: Chain B: T.169, T.170, H.173, T.301, G.302 Chain C: I.457 Ligands: NAD.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.173, B:T.301 Water bridges: B:G.302 TRS.12: 7 residues within 4Å: Chain B: A.40, G.43, L.44, K.47, E.433, V.434, E.437 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.40, B:E.437 TRS.19: 7 residues within 4Å: Chain B: I.457 Chain C: T.169, T.170, H.173, T.301, G.302 Ligands: NAD.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.173, C:T.301 Water bridges: C:G.302 TRS.20: 5 residues within 4Å: Chain C: A.40, G.43, L.44, K.47, E.437 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.40, C:G.43, C:E.437 Water bridges: C:E.433, C:E.437 TRS.29: 7 residues within 4Å: Chain A: I.457 Chain D: T.169, T.170, H.173, T.301, G.302 Ligands: NAD.28 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.301 Water bridges: D:G.302 TRS.31: 6 residues within 4Å: Chain D: A.40, G.43, L.44, K.47, E.433, E.437 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.433, D:E.437, D:E.437

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: K.17, V.18, A.19, W.111, E.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.17, A:E.118 Water bridges: A:V.18 PEG.22: 5 residues within 4Å: Chain C: K.17, V.18, W.111, E.118 Ligands: PEG.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.17, C:E.118 PEG.23: 4 residues within 4Å: Chain C: K.17, E.118, W.121 Ligands: PEG.22 No protein-ligand interaction detected (PLIP) PEG.30: 4 residues within 4Å: Chain D: G.356, K.357, D.358, G.359 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.357, D:D.358, D:G.359

5 x K: POTASSIUM ION(Non-covalent)

K.6: 5 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 Ligands: ADN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.383, A:T.383, A:H.385, H2O.7, H2O.10 K.13: 5 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385 Ligands: ADN.9 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.24 K.24: 5 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385 Ligands: ADN.18 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.39, H2O.41 K.32: 5 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385 Ligands: ADN.27 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.52, H2O.55 K.33: 1 residues within 4Å: Chain D: D.358 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 6 residues within 4Å: Chain A: G.458, V.459, P.464, F.465, K.466, P.467 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.458 Water bridges: A:F.465, A:K.466 PO4.21: 2 residues within 4Å: Chain C: A.25, R.29 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:E.344, C:A.25, C:R.29 Hydrogen bonds: C:W.26 Salt bridges: C:R.29 PO4.25: 4 residues within 4Å: Chain C: G.458, P.464, K.466, P.467 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.458, C:K.466 Water bridges: C:K.466 PO4.34: 6 residues within 4Å: Chain D: G.458, V.459, P.464, F.465, K.466, P.467 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.464

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: R.216 Ligands: CL.15 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: T.450, P.451, K.452 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: R.216 Ligands: CL.8 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: K.466 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain C: R.216 Ligands: CL.35 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain D: R.216 Ligands: CL.26 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain D: R.29 Ligands: CL.37 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain D: A.25, R.29 Ligands: CL.36 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain D: K.17, V.18 Ligands: CL.39 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain D: K.17, W.111 Ligands: CL.38 Ligand excluded by PLIP

Links

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Citation

Drozdzal, P. et al., Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations. To Be Published

Release Date

2023-08-16

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Adenosylhomocysteinase