SMTL ID : 9hkz.1

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 closed subunits

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: C.206, 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, H.385 Chain D: L.449, Q.453, K.466, Y.470 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:D.234, A:V.255, A:D.256, A:T.301, A:N.303, A:H.326, A:H.385, D:Q.453, D:K.466, D:K.466 NAD.2: 19 residues within 4Å: Chain B: I.230, G.231, Y.232, G.233, D.234, V.235, E.254, V.255, D.256, C.259, T.300, T.301, N.303, V.306, H.326 Chain C: L.449, Q.453, K.466, Y.470 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:K.466, C:K.466, C:Y.470, C:Y.470, B:Y.232, B:D.234, B:T.300, B:T.301, B:N.303, B:H.326 Salt bridges: C:K.466 NAD.3: 21 residues within 4Å: Chain B: L.449, Q.453, K.466, Y.470 Chain C: N.202, G.233, D.234, V.235, E.254, V.255, D.256, C.259, T.300, T.301, N.303, V.306, I.324, G.325, H.326, L.376, N.378 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.235 Hydrogen bonds: C:D.234, C:V.235, C:V.255, C:D.256, C:I.324, C:N.378, B:Q.453, B:K.466, B:K.466, B:Y.470, B:Y.470 NAD.4: 24 residues within 4Å: Chain A: T.447, L.449, Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, N.202, G.233, D.234, V.235, E.254, V.255, D.256, C.259, T.301, N.303, I.324, H.326, L.376, N.378, H.385 Ligands: ADN.5 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:N.202 Hydrogen bonds: 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:H.326, D:N.378, D:H.385, A:Q.453, A:K.466, A:K.466, A:Y.470 Salt bridges: A:K.466

1 x ADN: ADENOSINE(Non-covalent)

ADN.5: 15 residues within 4Å: Chain D: I.63, H.64, T.66, Q.68, T.69, D.142, E.167, T.168, K.197, D.201, H.326, L.376, H.385, M.390 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.68, D:T.69, D:T.168, D:T.168, D:K.197, D:H.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 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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