SMTL ID : 8cfu.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H02

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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, PO4.8 25 PLIP interactions: 4 interactions with chain D, 21 interactions with chain A Hydrogen bonds: D:Q.453, D:Q.453, D:K.466, D:K.466, A:T.169, A:T.169, 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 Hydrophobic interactions: A:N.202, A:V.235 Water bridges: A:N.192, A:G.236, A:F.327, A:E.330 NAD.11: 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.12, PO4.18 26 PLIP interactions: 4 interactions with chain C, 22 interactions with chain B Hydrogen bonds: C:Q.453, C:Q.453, C:K.466, C:K.466, 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 Hydrophobic interactions: B:N.202, B:V.235 Water bridges: B:D.234, B:D.234, B:G.236, B:F.327, B:E.330 NAD.20: 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.21, PO4.25 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: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:T.169, C:N.192, C:G.236, C:F.327, C:E.330 NAD.27: 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: ADE.28, PO4.32 27 PLIP interactions: 20 interactions with chain D, 7 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, A:Y.470 Water bridges: D:N.192, D:G.236, D:F.327, D:E.330 Salt bridges: A:K.466

4 x ADE: ADENINE(Non-covalent)

ADE.2: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.69, 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: NAD.11, PO4.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.385 ADE.21: 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.20, PO4.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: 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, PO4.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.68, D:H.385

2 x RDV: 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one(Non-covalent)

RDV.3: 4 residues within 4Å: Chain A: H.151, K.152, P.155, M.178 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.151, A:K.152 RDV.13: 6 residues within 4Å: Chain B: A.40, L.44, K.47, E.433, V.434, E.437 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.40

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

DMS.4: 8 residues within 4Å: Chain A: D.468, T.469, Y.470, R.471 Chain D: D.468, T.469, Y.470, R.471 No protein-ligand interaction detected (PLIP) DMS.22: 8 residues within 4Å: Chain B: D.468, T.469, Y.470, R.471 Chain C: D.468, T.469, Y.470, R.471 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 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.8 K.16: 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.26 K.23: 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.41, H2O.41 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.53, H2O.56

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

PO4.6: 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:L.315, A:K.317 Water bridges: A:K.317 Salt bridges: A:R.354 PO4.7: 5 residues within 4Å: Chain A: R.28, I.32, E.35, E.74 Chain B: H.363 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.35, A:E.35 Water bridges: A:R.45, A:R.45 Salt bridges: A:R.28, B:H.363 PO4.8: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.142, A:E.167, A:T.168, A:D.201, A:D.201 Salt bridges: A:K.197 PO4.9: 6 residues within 4Å: Chain A: G.458, V.459, P.464, F.465, K.466, P.467 No protein-ligand interaction detected (PLIP) PO4.17: 6 residues within 4Å: Chain B: K.313, A.314, L.315, K.316, K.317, R.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.314, B:L.315, B:K.317 Salt bridges: B:R.354 PO4.18: 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:H.64, B:T.168, B:D.201, B:D.201 Salt bridges: B:K.197 PO4.19: 6 residues within 4Å: Chain B: G.458, V.459, P.464, F.465, K.466, P.467 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.458, B:F.465, B:K.466 PO4.24: 6 residues within 4Å: Chain C: K.313, A.314, L.315, K.316, K.317, R.354 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.317 Water bridges: C:K.313, C:R.354, C:R.354, C:D.366 Salt bridges: C:R.354 PO4.25: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.20, ADE.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.168, C:H.385 Salt bridges: C:K.197 PO4.26: 5 residues within 4Å: Chain C: G.458, V.459, P.464, K.466, P.467 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.458, C:F.465, C:K.466 Water bridges: C:D.468 PO4.31: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.317 Water bridges: D:A.314 Salt bridges: D:R.354 PO4.32: 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:E.167, D:E.167, D:E.167 Water bridges: D:T.168, D:T.168 Salt bridges: D:K.197 PO4.33: 5 residues within 4Å: Chain D: G.458, V.459, P.464, K.466, P.467 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.458, D:D.468

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain A: D.219, K.346 Chain B: W.26, E.30, Q.94, Q.96, R.216, T.383 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.30, B:Q.94, B:Q.96, B:R.216, A:K.346, A:K.346 Water bridges: B:D.95, A:D.219, A:D.219 GOL.14: 4 residues within 4Å: Chain B: S.460, E.462, G.463, P.464 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.460, B:E.462, B:G.463 GOL.15: 6 residues within 4Å: Chain B: A.24, A.25, R.28, A.100, A.103, A.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.24, B:R.28, B:A.100 GOL.29: 7 residues within 4Å: Chain C: D.219, K.346 Chain D: W.26, E.30, Q.94, Q.96, T.383 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:K.346, D:E.30, D:Q.94, D:Q.96 Water bridges: D:D.95, D:R.216

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 H02. To be published

Release Date

2024-02-21

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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