SMTL ID : 8cfz.2 (1 other biounit)

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 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 D: L.449, Q.453, K.466, Y.470 Ligands: ADE.2, PO4.5 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: 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, D:Y.470 Water bridges: A:N.192, A:G.236, A:F.327, A:E.330 NAD.8: 32 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: ADE.9, PO4.11 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.235 Hydrogen bonds: B:T.169, 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:H.326, B:N.378, B:N.378, C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470 Water bridges: B:T.169, B:N.192, B:G.236, B:F.327, B:E.330 NAD.15: 32 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, 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: ADE.16, PO4.23 26 PLIP interactions: 22 interactions with chain C, 4 interactions with chain B 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, B:Q.453, B:Q.453, B:K.466, B:K.466 Water bridges: C:G.233, C:D.234, C:D.234, C:G.236, C:F.327, C:E.330 NAD.27: 31 residues within 4Å: Chain A: L.449, 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, N.378, H.385 Ligands: ADE.28, PO4.31 27 PLIP interactions: 22 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:N.202, D:V.235 Hydrogen bonds: D:T.169, 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, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470 Water bridges: D:N.192, D:D.234, D:G.236, D:F.327, D:E.330

4 x ADE: ADENINE(Non-covalent)

ADE.2: 13 residues within 4Å: Chain A: I.63, H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.1, PO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68, A:H.385 ADE.9: 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: NAD.8, PO4.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 ADE.16: 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: NAD.15, PO4.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:T.69, C:H.385 ADE.28: 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: NAD.27, PO4.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385

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

PO4.3: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.363, A:R.28 Water bridges: A:R.45 PO4.4: 6 residues within 4Å: Chain A: K.313, A.314, L.315, K.316, K.317, R.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.317 Water bridges: A:R.354, A:D.366 Salt bridges: A:R.354 PO4.5: 10 residues within 4Å: Chain A: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.1, ADE.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.167, A:E.167, A:H.385 Salt bridges: A:K.197 PO4.6: 6 residues within 4Å: Chain A: G.458, V.459, P.464, F.465, K.466, P.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.465 Water bridges: A:D.468 PO4.10: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:E.35, B:R.45, B:R.45, B:E.74 Salt bridges: B:R.28, A:H.363 PO4.11: 10 residues within 4Å: Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.8, ADE.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.168, B:H.385 Water bridges: B:T.168, B:T.168 Salt bridges: B:K.197 PO4.12: 6 residues within 4Å: Chain B: G.458, V.459, P.464, F.465, K.466, P.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.464, B:K.466 Water bridges: B:S.460, B:P.464 PO4.21: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.35 Water bridges: C:R.45, C:R.45 Salt bridges: C:R.28, D:H.363 PO4.22: 6 residues within 4Å: Chain C: K.313, A.314, L.315, K.316, K.317, R.354 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.315, C:K.317 Water bridges: C:K.317 Salt bridges: C:R.354 PO4.23: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.15, ADE.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.168, C:D.201, C:D.201 Salt bridges: C:K.197 PO4.24: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.458, C:P.464 PO4.29: 5 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35, E.74 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.35, D:E.35 Water bridges: D:R.45, D:R.45 Salt bridges: D:R.28, C:H.363 PO4.30: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.317 Salt bridges: D:R.354 PO4.31: 10 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.27, ADE.28 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.64, D:E.167, D:T.168, D:D.201, D:D.201 Salt bridges: D:K.197

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.6, H2O.7 K.13: 5 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.383, B:T.383, B:H.385, H2O.19, H2O.23 K.25: 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.34, H2O.38 K.32: 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.53, H2O.54

2 x 01: 1-[2,4-bis(fluoranyl)phenyl]-2-(3,4-dihydro-1,2,4-triazol-2-yl)ethanone

01.14: 9 residues within 4Å: Chain B: D.468, T.469, Y.470, R.471 Chain C: V.425, D.468, T.469, Y.470, R.471 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:R.471, B:R.471 Hydrophobic interactions: C:R.471 01.26: 8 residues within 4Å: Chain A: V.425, D.468, T.469, R.471 Chain D: D.468, T.469, Y.470, R.471 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Water bridges: D:R.471, D:R.471, D:R.471, D:R.471 Hydrophobic interactions: A:T.469

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain B: P.257 Chain C: E.433, E.462, F.465 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:V.255, C:V.461 GOL.18: 6 residues within 4Å: Chain C: A.40, G.43, L.44, K.47, E.433, E.437 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.40, C:K.47 Water bridges: C:K.47, C:E.433, C:E.437 GOL.19: 4 residues within 4Å: Chain C: T.355, G.356, G.359 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.355 GOL.20: 4 residues within 4Å: Chain C: K.357, D.358, G.359 Ligands: GOL.19 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.357, C:D.358, C:D.358, C:G.359 Water bridges: C:D.358, C:D.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry H09. To be published

Release Date

2024-05-22

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

Adenosylhomocysteinase

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