SMTL ID : 7zd0.1

Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Cd2+ ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 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 D: L.449, Q.453, K.466, Y.470 Ligands: ADN.2 23 PLIP interactions: 19 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:N.202, A:G.233, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:H.326, A:N.378, A:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466 Water bridges: A:N.192, A:G.236, A:F.327, A:E.330 NAD.13: 31 residues within 4Å: 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 Chain C: L.449, Q.453, K.466, Y.470 Ligands: ADN.14 26 PLIP interactions: 5 interactions with chain C, 21 interactions with chain B Hydrogen bonds: C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470, B:T.169, B:T.170, B:T.170, B:T.170, B:N.202, B:G.233, B:D.234, B:V.235, B:V.255, B:D.256, B:N.303, B:I.324, B:H.326, B:N.378 Hydrophobic interactions: B:N.202, B:V.235 Water bridges: B:T.169, B:D.234, B:G.236, B:F.327, B:E.330 NAD.22: 30 residues within 4Å: Chain B: Q.453, K.466, Y.470 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 Ligands: ADN.23 25 PLIP interactions: 4 interactions with chain B, 21 interactions with chain C Hydrogen bonds: B:Q.453, B:Q.453, B:K.466, B:K.466, C:T.169, C:T.169, 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:H.326, C:N.378, C:N.378 Hydrophobic interactions: C:N.202, C:V.235 Water bridges: C:D.234, C:D.234, C:G.236, C:F.327, C:E.330 NAD.32: 30 residues within 4Å: Chain A: 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: ADN.33 27 PLIP interactions: 6 interactions with chain A, 21 interactions with chain D Hydrogen bonds: A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470, D:T.169, D:T.170, D:T.170, D:T.170, D:N.202, D:G.233, 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:D.234, D:D.234, D:G.236, D:F.327, D:E.330

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 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, CD.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.168, A:K.197, A:K.197, A:H.326, A:H.385 ADN.14: 19 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.13, CD.17 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.68, B:T.69, B:E.167, B:T.168, B:T.168, B:K.197, B:K.197, B:H.326, B:H.385 Water bridges: B:D.142 ADN.23: 19 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.22, CD.28 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:T.168, C:K.197, C:K.197, C:H.385 Water bridges: C:H.64, C:H.326 ADN.33: 19 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.32, CD.37 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.68, D:T.69, D:E.167, D:T.168, D:T.168, D:K.197, D:K.197, D:H.326, D:H.385

6 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 5 residues within 4Å: Chain A: K.17, V.18, A.19, W.111 Ligands: PDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.111 BU1.4: 5 residues within 4Å: Chain A: E.148, H.151, K.152, M.178, T.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.152 Water bridges: A:K.152 BU1.24: 3 residues within 4Å: Chain C: K.17, V.18, W.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.17, C:E.118 Water bridges: C:V.18 BU1.25: 2 residues within 4Å: Chain C: T.14, Y.16 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.16 BU1.26: 3 residues within 4Å: Chain C: H.151, K.152, M.178 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:H.151, C:K.152 Hydrogen bonds: C:K.152 Water bridges: C:E.148, C:E.148 BU1.34: 3 residues within 4Å: Chain D: K.17, V.18, W.111 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.17 Water bridges: D:V.18

2 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.5: 3 residues within 4Å: Chain A: N.276, I.278 Chain D: Q.448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.276 PDO.6: 4 residues within 4Å: Chain A: T.14, Y.16, K.17 Ligands: BU1.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.14

4 x K: POTASSIUM ION(Non-covalent)

K.7: 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.7, H2O.11 K.16: 5 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385, P.386 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.383, B:T.383, B:H.385, H2O.25 K.27: 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.41, H2O.41 K.35: 5 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.57, H2O.57

19 x CD: CADMIUM ION(Non-covalent)

CD.8: 4 residues within 4Å: Chain A: C.88, D.142, H.326 Ligands: ADN.2 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: H.173 Chain D: Y.456 Ligand excluded by PLIP CD.10: 1 residues within 4Å: Chain A: H.403 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain A: D.361, H.363 Ligand excluded by PLIP CD.12: 1 residues within 4Å: Chain A: E.406 Ligand excluded by PLIP CD.17: 4 residues within 4Å: Chain B: C.88, D.142, H.326 Ligands: ADN.14 Ligand excluded by PLIP CD.18: 1 residues within 4Å: Chain B: H.403 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain B: H.173 Chain C: Y.456 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain B: E.406 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain A: E.35 Chain B: H.363 Ligand excluded by PLIP CD.28: 4 residues within 4Å: Chain C: C.88, D.142, H.326 Ligands: ADN.23 Ligand excluded by PLIP CD.29: 2 residues within 4Å: Chain C: H.403, E.424 Ligand excluded by PLIP CD.30: 2 residues within 4Å: Chain B: Y.456 Chain C: H.173 Ligand excluded by PLIP CD.31: 2 residues within 4Å: Chain C: D.361, H.363 Ligand excluded by PLIP CD.36: 2 residues within 4Å: Chain D: D.361, H.363 Ligand excluded by PLIP CD.37: 4 residues within 4Å: Chain D: C.88, D.142, H.326 Ligands: ADN.33 Ligand excluded by PLIP CD.38: 1 residues within 4Å: Chain D: H.403 Ligand excluded by PLIP CD.39: 2 residues within 4Å: Chain A: Y.456 Chain D: H.173 Ligand excluded by PLIP CD.40: 1 residues within 4Å: Chain D: E.406 Ligand excluded by PLIP

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.15: 3 residues within 4Å: Chain B: K.17, V.18, W.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.17

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

CL.41: 3 residues within 4Å: Chain D: T.450, P.451, K.452 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Cd2+ ions. To Be Published

Release Date

2023-04-19

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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