SMTL ID : 9hkx.1

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 1 open and 3 closed subunits

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: 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, N.378, H.385 Chain B: L.449, K.466, Y.470 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.234, A:V.235, A:V.255, A:D.256, A:T.301, A:T.301, A:N.303, A:H.326, A:H.385, B:K.466, B:K.466, B:Y.470 NAD.2: 29 residues within 4Å: Chain A: T.447, L.449, K.466, Y.470 Chain B: 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, C.259, T.300, T.301, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Ligands: ADN.3 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.168, B:T.170, B:D.234, B:V.255, B:N.303, B:H.326, B:N.378, B:N.378, A:T.447, A:K.466, A:K.466, A:Y.470 NAD.5: 26 residues within 4Å: Chain C: T.168, T.169, T.170, N.202, C.206, I.230, G.231, Y.232, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.301, G.302, N.303, I.324, L.376, N.378 Chain D: L.449, Q.453, K.466, Y.470 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.169, C:T.170, C:T.170, C:T.170, C:Y.232, C:Y.232, C:D.234, C:V.235, C:V.255, C:T.301, C:N.303, C:I.324, C:N.378, D:Q.453, D:K.466, D:K.466, D:Y.470, D:Y.470 NAD.7: 22 residues within 4Å: Chain C: L.449, K.466, Y.470 Chain D: T.169, T.170, N.202, Y.232, G.233, D.234, V.235, E.254, V.255, D.256, T.301, N.303, V.306, I.324, H.326, L.376, N.378, H.385 Ligands: ADN.8 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:T.170, D:T.170, D:Y.232, D:D.234, D:V.235, D:V.255, D:N.303, D:H.326, D:N.378, D:N.378, C:K.466, C:K.466, C:Y.470, C:Y.470

2 x ADN: ADENOSINE(Non-covalent)

ADN.3: 15 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, H.385, M.390 Ligands: NAD.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.64, B:T.66, B:Q.68, B:E.167, B:T.168, B:K.197, B:H.385 pi-Stacking: B:H.64 ADN.8: 15 residues within 4Å: Chain D: I.63, H.64, T.66, Q.68, T.69, D.142, E.167, T.168, D.201, H.326, L.376, L.379, H.385, M.390 Ligands: NAD.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.66, D:D.201

3 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain B: Q.68, T.383, H.385 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.383, B:H.385 K.6: 3 residues within 4Å: Chain C: Q.68, Q.94, H.385 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain D: Q.68, T.383, H.385 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.383

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 1 open and 3 closed subunits. To Be Published

Release Date

2025-02-19

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Adenosylhomocysteinase

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