SMTL ID : 8cfn.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment F03

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 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.6, PO4.8 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:V.235 Hydrogen bonds: A:T.169, A:T.169, A:T.169, 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:D.234, A:G.236, A:F.327, A:E.330 NAD.9: 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.18, PO4.19 27 PLIP interactions: 21 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.169, 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, C:Y.470 Water bridges: B:N.192, B:G.236, B:F.327, B:E.330 NAD.21: 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.26, PO4.28 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.235 Hydrogen bonds: C:T.169, 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, 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.29: 32 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, L.376, N.378, H.385 Ligands: ADE.38, PO4.39 26 PLIP interactions: 21 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.169, 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 K: POTASSIUM ION(Non-covalent)

K.2: 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.8, H2O.8 K.10: 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.25, H2O.27 K.22: 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.44, H2O.44 K.30: 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.61, H2O.63

12 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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:E.35, A:R.45, A:R.45, A:R.45 Salt bridges: A:R.28, B:H.363 PO4.7: 6 residues within 4Å: Chain A: K.313, A.314, L.315, K.316, K.317, R.354 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.317 Water bridges: A:K.317, A:K.317 Salt bridges: A:K.317, A:R.354 PO4.8: 9 residues within 4Å: Chain A: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.1, ADE.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.64, A:E.167, A:T.168 Water bridges: A:K.197, A:K.197 Salt bridges: A:K.197 PO4.11: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 7 PLIP interactions: 5 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, A:H.363 Salt bridges: B:R.28, A:H.363 PO4.19: 9 residues within 4Å: Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.9, ADE.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.168, B:T.168, B:D.201 Water bridges: B:K.197, B:K.197 Salt bridges: B:K.197 PO4.20: 6 residues within 4Å: Chain B: K.203, Y.204 Chain C: K.203, K.237, Q.262, D.266 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Q.262 Water bridges: C:K.203, C:K.203, B:K.203, B:K.203, B:K.203 Salt bridges: C:K.203, B:K.203 PO4.23: 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:E.35, C:R.45, C:R.45, C:R.45 Salt bridges: C:R.28, D:H.363 PO4.27: 6 residues within 4Å: Chain C: K.313, A.314, L.315, K.316, K.317, R.354 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.317 Water bridges: C:K.317, C:K.317 Salt bridges: C:K.317, C:R.354 PO4.28: 9 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.21, ADE.26 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.64, C:E.167, C:T.168 Water bridges: C:K.197, C:K.197, C:H.326 Salt bridges: C:K.197 PO4.31: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Water bridges: C:H.363, D:R.45, D:R.45 Salt bridges: C:H.363, D:R.28 Hydrogen bonds: D:E.35, D:E.35 PO4.39: 9 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.29, ADE.38 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.168, D:T.168, D:D.201 Water bridges: D:K.197, D:K.197 Salt bridges: D:K.197 PO4.40: 6 residues within 4Å: Chain A: K.203, K.237, Q.262, D.266 Chain D: K.203, Y.204 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:Q.262, D:Y.204 Water bridges: A:K.203, A:K.203, D:K.203, D:K.203, D:K.203 Salt bridges: A:K.203, D:K.203

4 x RAY: N-(3-fluorophenyl)-2-(2-methoxyethoxy)acetamide(Non-covalent)

RAY.4: 9 residues within 4Å: Chain A: Y.48, I.189, L.399, I.402, H.403, E.424, L.426, P.427, L.430 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.189, A:H.403, A:L.426, A:P.427, A:L.430 Hydrogen bonds: A:H.403 pi-Stacking: A:H.403 RAY.12: 8 residues within 4Å: Chain B: Y.48, L.399, I.402, H.403, V.425, L.426, P.427, L.430 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.403, B:L.426, B:P.427, B:L.430 pi-Stacking: B:H.403 RAY.24: 9 residues within 4Å: Chain C: Y.48, I.189, L.399, I.402, H.403, E.424, L.426, P.427, L.430 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.189, C:H.403, C:L.426, C:P.427, C:L.430 Water bridges: C:H.403 pi-Stacking: C:H.403 RAY.32: 8 residues within 4Å: Chain D: Y.48, L.399, I.402, H.403, V.425, L.426, P.427, L.430 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:H.403, D:L.426, D:P.427, D:L.430 Water bridges: D:H.403 pi-Stacking: D:H.403

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 5 residues within 4Å: Chain A: V.459, P.464, F.465, K.466, P.467 No protein-ligand interaction detected (PLIP) DMS.13: 5 residues within 4Å: Chain B: K.313, A.314, L.315, K.317, R.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.354, B:R.354 Salt bridges: B:D.366 DMS.15: 5 residues within 4Å: Chain B: G.458, V.459, P.464, K.466, P.467 No protein-ligand interaction detected (PLIP) DMS.16: 4 residues within 4Å: Chain B: K.17, V.18, W.111, E.118 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.111, B:W.111 DMS.25: 5 residues within 4Å: Chain C: V.459, P.464, F.465, K.466, P.467 No protein-ligand interaction detected (PLIP) DMS.33: 5 residues within 4Å: Chain D: K.313, A.314, L.315, K.317, R.354 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.354, D:R.354 Salt bridges: D:D.366 DMS.35: 5 residues within 4Å: Chain D: G.458, V.459, P.464, K.466, P.467 No protein-ligand interaction detected (PLIP) DMS.36: 4 residues within 4Å: Chain D: K.17, V.18, W.111, E.118 2 PLIP interactions: 2 interactions with chain D pi-Cation interactions: D:W.111, D:W.111

4 x ADE: ADENINE(Non-covalent)

ADE.6: 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: NAD.1, PO4.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385 Water bridges: A:D.201 ADE.18: 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.9, PO4.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 Water bridges: B:D.201 ADE.26: 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.21, PO4.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.68, C:H.385 Water bridges: C:D.201 ADE.38: 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.29, PO4.39 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385 Water bridges: D:D.201

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain B: K.112, G.113, P.347, Q.348 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.348 GOL.17: 2 residues within 4Å: Chain B: D.361, H.363 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.361, B:H.363 GOL.34: 4 residues within 4Å: Chain D: K.112, G.113, P.347, Q.348 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.348 GOL.37: 2 residues within 4Å: Chain D: D.361, H.363 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.361, D:H.363, D:H.363

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 F03. To be published

Release Date

2024-02-21

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Adenosylhomocysteinase

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