SMTL ID : 9hkw.1

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 3 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: I.230, G.231, G.233, D.234, V.235, E.254, V.255, D.256, T.300, T.301, G.302, N.303, V.306, I.324, H.326, N.378, H.385 Chain D: L.449, Q.453, K.466, Y.470 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:D.234, A:V.235, A:V.255, A:D.256, A:T.301, A:H.326, A:N.378, A:N.378, D:Q.453, D:K.466, D:K.466, D:Y.470 NAD.2: 24 residues within 4Å: Chain B: D.201, N.202, C.206, I.230, G.231, Y.232, G.233, D.234, V.235, E.254, V.255, D.256, T.300, T.301, N.303, V.306, G.325, H.326, L.376, H.385 Chain C: L.449, Q.453, K.466, Y.470 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Y.232, B:Y.232, B:D.234, B:V.235, B:V.255, B:D.256, B:T.301, B:N.303, C:K.466, C:K.466, C:Y.470, C:Y.470 NAD.3: 22 residues within 4Å: Chain B: Q.453, K.466, Y.470 Chain C: N.202, I.230, G.231, G.233, D.234, V.235, E.254, V.255, D.256, C.259, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:D.234, C:V.235, C:V.255, C:D.256, C:T.301, C:N.303, C:I.324, C:N.378, B:K.466, B:K.466, B:Y.470, B:Y.470 NAD.4: 27 residues within 4Å: Chain A: L.449, K.466, Y.470 Chain D: T.168, T.169, T.170, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Ligands: ADN.5 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.202, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:I.324, D:N.378, A:K.466, A:K.466, A:Y.470

1 x ADN: ADENOSINE(Non-covalent)

ADN.5: 11 residues within 4Å: Chain D: H.64, T.66, Q.68, D.142, T.168, K.197, D.201, H.326, H.385, M.390 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.66, D:T.168, D:K.197, D:D.201, D:H.385

1 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain D: Q.68, T.383, H.385 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.383, D:T.383, 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 3 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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