SMTL ID : 7zd4.1

Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase soaked with Cu+ ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 32 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: L.449, Q.453, K.466, Y.470 Ligands: ADN.2, MPD.3 26 PLIP interactions: 21 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.170, A:T.170, A:N.202, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:H.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.5: 32 residues within 4Å: Chain B: T.168, T.169, T.170, D.201, N.202, C.206, I.230, G.231, G.233, D.234, V.235, 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: L.449, Q.453, K.466, Y.470 Ligands: ADN.6, MPD.7 27 PLIP interactions: 21 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: 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:H.326, 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:T.169, B:N.192, B:G.233, B:G.236, B:F.327, B:E.330 NAD.9: 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.10 26 PLIP interactions: 5 interactions with chain B, 21 interactions with chain C Hydrogen bonds: B:Q.453, B:Q.453, B:K.466, B:K.466, B:Y.470, 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:H.326, C:N.378, C:N.378 Hydrophobic interactions: C:N.202, C:V.235 Water bridges: C:D.234, C:D.234, C:G.236, C:G.325, C:F.327 NAD.13: 32 residues within 4Å: Chain A: L.449, Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, D.201, N.202, C.206, 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.14 27 PLIP interactions: 21 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:N.202, D:V.235 Hydrogen bonds: D:T.169, D:T.170, 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:H.326, 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:D.234, D:D.234, D:G.236, D:F.327, D:E.330

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 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.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.168, A:K.197, A:K.197, A:H.326, A:H.385 ADN.6: 18 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.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.5, K.8 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.10: 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.9, K.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:T.168, C:K.197, C:K.197, C:H.326, C:H.385 ADN.14: 19 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.13, K.16 9 PLIP interactions: 9 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.326, D:H.385

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 7 residues within 4Å: Chain A: T.169, T.170, H.173, T.301, G.302 Chain D: I.457 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.301 MPD.7: 7 residues within 4Å: Chain B: T.169, T.170, H.173, T.301, G.302 Chain C: I.457 Ligands: NAD.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.173 Water bridges: B:T.301 MPD.11: 7 residues within 4Å: Chain B: Y.456, I.457 Chain C: T.169, T.170, H.173, T.301, G.302 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.169, C:H.173, B:Y.456, B:I.457 MPD.15: 6 residues within 4Å: Chain A: I.457 Chain D: T.169, T.170, H.173, T.301, G.302 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.173

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 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.7 K.8: 5 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385 Ligands: ADN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.383, B:T.383, B:H.385, H2O.17, H2O.18 K.12: 5 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385 Ligands: ADN.10 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.32, H2O.36 K.16: 6 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385, P.386 Ligands: ADN.14 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.46, H2O.50

1 x BR: BROMIDE ION(Non-covalent)

BR.17: 3 residues within 4Å: Chain D: T.450, P.451, K.452 Ligand excluded by PLIP

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 soaked with Cu+ ions. To Be Published

Release Date

2023-04-19

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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