SMTL ID : 8ajs.1

Crystal structure of the F324A 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 1.68 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 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, H.326, L.376, N.378, H.385 Chain D: Q.453, K.466, Y.470 Ligands: ADN.2 22 PLIP interactions: 18 interactions with chain A, 4 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:N.202, A:G.233, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:N.378, A:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466 Water bridges: A:D.234, A:D.234, A:G.236 NAD.4: 30 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, H.326, L.376, N.378, H.385 Chain C: Q.453, K.466, Y.470 Ligands: ADN.5 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.169, B:T.169, B:T.170, B:T.170, B:N.202, B:G.233, 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 Water bridges: B:D.234, B:D.234, B:G.236 NAD.8: 31 residues within 4Å: Chain B: L.449, 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, H.326, L.376, N.378, H.385 Ligands: ADN.9 23 PLIP interactions: 19 interactions with chain C, 4 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:T.170, C:N.202, C:G.233, C:D.234, C:V.235, C:V.255, C:D.256, C:N.303, C:N.378, C:N.378, B:Q.453, B:Q.453, B:K.466, B:K.466 Water bridges: C:D.234, C:D.234, C:G.236 NAD.12: 30 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, H.326, L.376, N.378, H.385 Ligands: ADN.13 25 PLIP interactions: 19 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:N.202, D:V.235 Hydrogen bonds: D:T.169, D:T.169, D:T.169, D:T.170, D:T.170, D:N.202, D:G.233, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:N.378, D:N.378, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470 Water bridges: D:T.168, D:N.192, D:G.236

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 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.1, K.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:K.197, A:K.197, A:H.385 ADN.5: 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.4, K.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.68, B:T.69, B:E.167, B:K.197, B:K.197, B:H.385 ADN.9: 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.8, K.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:K.197, C:K.197, C:H.385 Water bridges: C:G.325 ADN.13: 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.12, K.14 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.68, D:T.69, D:E.167, D:K.197, D:K.197, D:H.385

4 x K: POTASSIUM ION(Non-covalent)

K.3: 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.9, H2O.10 K.6: 6 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385, P.386 Ligands: ADN.5 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.23 K.11: 5 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385 Ligands: ADN.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.41, H2O.42 K.14: 6 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385, P.386 Ligands: ADN.13 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.57, H2O.58

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

CL.7: 3 residues within 4Å: Chain B: T.450, P.451, K.452 Ligand excluded by PLIP

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

PEG.10: 4 residues within 4Å: Chain C: R.337, W.342, H.350, E.373 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.337, C:R.337 Water bridges: C:R.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drozdzal, P. et al., Crystal structure of the F324A 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