SMTL ID : 9hky.1

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 open and 2 closed subunits

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: I.230, G.233, D.234, V.235, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, G.325, H.326, F.327 Chain D: L.449, K.466, Y.470 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:D.234, A:V.235, A:V.255, A:D.256, A:T.301, A:N.303, D:Q.453, D:K.466 pi-Cation interactions: A:H.326 Salt bridges: D:K.466 NAD.2: 23 residues within 4Å: Chain B: T.169, T.170, N.202, I.230, G.231, G.233, D.234, V.235, E.254, V.255, D.256, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376 Chain C: Q.453, K.466, Y.470 Ligands: ADN.3 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Q.453, C:K.466, C:K.466, C:Y.470, B:D.234, B:V.235, B:V.255, B:T.301, B:N.303 Salt bridges: C:K.466 NAD.5: 19 residues within 4Å: Chain B: L.449, K.466, Y.470 Chain C: N.202, C.206, I.230, Y.232, G.233, D.234, V.235, E.254, V.255, D.256, T.301, N.303, V.306, I.324, H.326, H.385 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:Y.470, C:Y.232, C:D.234, C:V.235, C:V.255, C:D.256, C:T.301, C:N.303, C:I.324 Salt bridges: B:K.466 Hydrophobic interactions: C:V.235 NAD.6: 25 residues within 4Å: Chain A: Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, N.202, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, V.306, I.324, H.326, L.376, H.385 Ligands: ADN.7 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:V.235 Hydrogen bonds: D:T.168, D:T.169, D:T.170, D:N.202, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:I.324, D:H.326, D:N.378, A:T.447, A:Q.453, A:K.466, A:K.466, A:Y.470

2 x ADN: ADENOSINE(Non-covalent)

ADN.3: 11 residues within 4Å: Chain B: H.64, T.66, T.69, E.167, T.168, K.197, D.201, L.379, H.385, M.390 Ligands: NAD.2 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.197, B:D.201, B:H.385 pi-Stacking: B:H.64, B:H.64, B:H.385 ADN.7: 14 residues within 4Å: Chain D: I.63, H.64, T.66, Q.68, T.69, T.168, K.197, D.201, H.326, L.376, L.379, H.385, M.390 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.66, D:T.66, D:T.69, D:T.168, D:K.197, D:D.201, D:H.385

2 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain B: Q.68, T.383, H.385 No protein-ligand interaction detected (PLIP) K.8: 4 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.383, D:H.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Cryo-EM struture of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 open and 2 closed subunits. To Be Published

Release Date

2025-02-19

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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