SMTL ID : 6f3p.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 33 residues within 4Å: Chain A: 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 Chain D: L.449, Q.453, K.466, Y.470 Ligands: 3AD.2, CL.4 27 PLIP interactions: 23 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:N.202, A:V.235 Hydrogen bonds: A:T.169, A:T.170, A:T.170, A:T.170, A:N.202, A:G.233, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:I.324, A:H.326, A:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466 Water bridges: A:T.169, A:T.169, A:N.192, A:D.234, A:G.236, A:E.330, A:E.330 NAD.6: 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, 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 C: Q.453, K.466, Y.470 Ligands: 3AD.7, CL.9 26 PLIP interactions: 20 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:I.324, B:H.326, B:N.378, C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470, C:Y.470 Water bridges: B:N.192, B:G.233, B:G.236, B:F.327, B:E.330 NAD.11: 33 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, 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: 3AD.12, CL.14 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:N.202, C:V.235 Hydrogen bonds: C:T.169, C:T.170, 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:I.324, C:H.326, C:N.378, B:Q.453, B:Q.453, B:K.466, B:K.466, B:Y.470 Water bridges: C:N.192, C:G.236, C:F.327, C:E.330 NAD.16: 32 residues within 4Å: Chain A: 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: 3AD.17, CL.19 28 PLIP interactions: 23 interactions with chain D, 5 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:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:I.324, D:H.326, D:N.378, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470 Water bridges: D:T.169, D:T.169, D:N.192, D:G.233, D:D.234, D:G.236, D:F.327, D:E.330

4 x 3AD: 3'-DEOXYADENOSINE(Non-covalent)

3AD.2: 18 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:K.197, A:K.197, A:H.326, A:H.385 3AD.7: 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.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.68, B:E.167, B:K.197, B:K.197, B:H.326, B:H.385 3AD.12: 18 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.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.68, C:E.167, C:K.197, C:K.197, C:H.326, C:H.385 3AD.17: 18 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.16 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:K.197, D:K.197, D:H.326, D:H.385

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.383, A:T.383, A:H.385, H2O.9, H2O.11 K.8: 4 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.383, B:T.383, B:H.385, H2O.30, H2O.32 K.13: 5 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.53, H2O.54 K.18: 4 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.73, H2O.75

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: T.168, T.169, N.192, K.197, N.202 Ligands: NAD.1 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: T.168, T.169, N.192, K.197, N.202 Ligands: NAD.6 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain C: T.168, T.169, N.192, K.197, N.202 Ligands: NAD.11 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain D: T.168, T.169, N.192, K.197, N.202 Ligands: NAD.16 Ligand excluded by PLIP

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:H.363, A:R.28 Water bridges: A:R.45, A:R.45, A:R.45, A:R.45 PO4.10: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.35, B:E.35 Water bridges: B:R.45, B:R.45, B:R.45, A:H.363 Salt bridges: B:R.28, A:H.363 PO4.15: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Water bridges: C:R.45, C:R.45, C:R.45, C:R.45 Salt bridges: C:R.28, D:H.363 PO4.20: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.35, D:E.35 Water bridges: D:R.45, D:R.45, D:R.45, C:H.363 Salt bridges: D:R.28, C:H.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czyrko, J. et al., Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep (2018)

Release Date

2018-08-08

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Adenosylhomocysteinase

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