SMTL ID : 6f3q.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenine and Rb+ cation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

5 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 4 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.383, A:T.383, A:H.385, H2O.11 RB.6: 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.30 RB.7: 2 residues within 4Å: Chain B: F.13, T.14 No protein-ligand interaction detected (PLIP) RB.13: 4 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.51, H2O.51 RB.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.70, H2O.72

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

PO4.2: 10 residues within 4Å: Chain A: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.4, ADE.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.64, A:E.167, A:T.168, A:D.201, A:D.201 Salt bridges: A:K.197 PO4.3: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain C: H.363 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.35, A:E.35 Water bridges: A:R.45, A:R.45 Salt bridges: A:R.28, C:H.363 PO4.8: 4 residues within 4Å: Chain B: R.28, I.32, E.35 Chain D: H.363 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Water bridges: B:R.28, B:E.35, B:R.45, B:R.45, B:R.45 Salt bridges: B:R.28, D:H.363 PO4.9: 10 residues within 4Å: Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.11, ADE.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.167, B:E.167, B:E.167, B:H.385 Salt bridges: B:K.197 PO4.14: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.16, ADE.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.168, C:D.201 Salt bridges: C:K.197 PO4.15: 4 residues within 4Å: Chain A: H.363 Chain C: R.28, I.32, E.35 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.45, C:R.45 Salt bridges: C:R.28, A:H.363 PO4.20: 4 residues within 4Å: Chain B: H.363 Chain D: R.28, I.32, E.35 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Water bridges: D:R.45, D:R.45 Salt bridges: D:R.28, B:H.363 PO4.21: 10 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.22, ADE.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.168 Water bridges: D:T.168 Salt bridges: D:K.197

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

NAD.4: 32 residues within 4Å: Chain A: T.168, T.169, T.170, D.201, 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, L.376, N.378, H.385 Chain B: L.449, Q.453, K.466, Y.470 Ligands: PO4.2, ADE.5 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.202, A:V.235 Hydrogen bonds: A:T.169, 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, B:Q.453, B:Q.453, B:K.466, B:K.466 Water bridges: A:N.192, A:G.236, A:H.326, A:F.327, A:E.330 Salt bridges: B:K.466 NAD.11: 32 residues within 4Å: Chain A: L.449, Q.453, K.466, Y.470 Chain B: T.168, T.169, T.170, D.201, 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, L.376, N.378, H.385 Ligands: PO4.9, ADE.12 27 PLIP interactions: 21 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.169, B:T.169, 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, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470 Water bridges: B:N.192, B:G.233, B:G.236, B:H.326, B:F.327, B:E.330 NAD.16: 32 residues within 4Å: Chain C: T.168, T.169, T.170, D.201, 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, L.376, N.378, H.385 Chain D: L.449, Q.453, K.466, Y.470 Ligands: PO4.14, ADE.17 27 PLIP interactions: 22 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:N.202, C:V.235 Hydrogen bonds: C:T.169, C:T.169, C:T.170, C:T.170, C:T.170, C:N.202, C:D.234, C:V.235, C:V.255, C:D.256, C:N.303, C:H.326, C:N.378, C:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466, D:Y.470 Water bridges: C:G.233, C:D.234, C:D.234, C:G.236, C:F.327, C:E.330 NAD.22: 31 residues within 4Å: Chain C: Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, D.201, 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, L.376, N.378, H.385 Ligands: PO4.21, ADE.23 27 PLIP interactions: 6 interactions with chain C, 21 interactions with chain D Hydrogen bonds: C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470, C:Y.470, 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:N.378 Hydrophobic interactions: D:N.202, D:V.235 Water bridges: D:T.168, D:G.233, D:D.234, D:D.234, D:G.236, D:F.327, D:E.330

4 x ADE: ADENINE(Non-covalent)

ADE.5: 12 residues within 4Å: Chain A: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: PO4.2, NAD.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:H.385 ADE.12: 12 residues within 4Å: Chain B: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: PO4.9, NAD.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 Water bridges: B:H.64 ADE.17: 12 residues within 4Å: Chain C: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: PO4.14, NAD.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:T.69, C:H.385 Water bridges: C:H.64 ADE.23: 12 residues within 4Å: Chain D: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: PO4.21, NAD.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.68, D:T.69, D:H.385 Water bridges: D:H.64

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 1 residues within 4Å: Chain B: T.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.22

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 2 residues within 4Å: Chain D: T.14, Y.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.16

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
B

C
C

D
D

Adenosylhomocysteinase

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