SMTL ID : 8cfb.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment D02

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 33 residues within 4Å: Chain A: 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 Chain D: L.449, Q.453, K.466, Y.470 Ligands: ADE.2, PO4.7 24 PLIP interactions: 19 interactions with chain A, 5 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, D:Y.470 Water bridges: A:N.192, 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, 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 Chain C: Q.453, K.466, Y.470 Ligands: ADE.10, PO4.14 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:V.235 Hydrogen bonds: B:T.168, 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: C:T.447 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, PO4.19 20 PLIP interactions: 16 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.235 Hydrogen bonds: C:T.169, C:T.169, C:T.170, 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 NAD.22: 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.23, PO4.27 27 PLIP interactions: 5 interactions with chain A, 22 interactions with chain D Hydrogen bonds: A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470, D:T.169, D:T.169, D:T.170, 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:N.192, D:G.233, 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, PO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:H.385 ADE.10: 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, PO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 ADE.16: 12 residues within 4Å: Chain C: T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.15, K.17, PO4.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:H.385 ADE.23: 13 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.22, K.24, PO4.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:H.385

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

DMS.3: 5 residues within 4Å: Chain A: D.468, T.469 Chain D: D.468, T.469, R.471 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.4: 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.2, H2O.12 K.11: 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.12, H2O.12 K.17: 4 residues within 4Å: Chain C: Q.68, T.383, H.385 Ligands: ADE.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.383, C:T.383, C:H.385 K.24: 4 residues within 4Å: Chain D: Q.68, T.383, H.385 Ligands: ADE.23 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.383, D:H.385, H2O.17

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

PO4.5: 5 residues within 4Å: Chain A: K.313, A.314, L.315, K.317, R.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.317 Salt bridges: A:R.354 PO4.6: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.363, A:R.28 Water bridges: A:E.35, A:R.45 PO4.7: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.201, A:D.201 Salt bridges: A:K.197 PO4.12: 5 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35, E.74 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.35, B:E.35 Salt bridges: B:R.28, A:H.363 PO4.13: 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:K.317 Water bridges: B:K.317 Salt bridges: B:R.354 PO4.14: 10 residues within 4Å: Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.9, ADE.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.167, B:T.168 Salt bridges: B:K.197 PO4.18: 6 residues within 4Å: Chain C: R.28, I.32, E.35, R.45, E.74 Chain D: H.363 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.35, C:R.45, C:E.74 Salt bridges: C:R.28, D:H.363 PO4.19: 8 residues within 4Å: Chain C: D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.15, ADE.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.167, C:T.168, C:T.168, C:D.201 Salt bridges: C:K.197 PO4.20: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 No protein-ligand interaction detected (PLIP) PO4.21: 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:L.315, C:K.317 Salt bridges: C:R.354 PO4.25: 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:L.315 Salt bridges: D:K.317, D:R.354 PO4.26: 5 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35, E.74 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.28, C:H.363 PO4.27: 9 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.22, ADE.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.64, D:T.168, D:D.201 Salt bridges: D:K.197 PO4.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.29: 5 residues within 4Å: Chain D: G.458, V.459, P.464, K.466, P.467 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.458, D:P.464 Water bridges: D:D.468

1 x SY4: ~{N}-[5-azanyl-2,4-bis(fluoranyl)phenyl]propane-1-sulfonamide(Non-covalent)

SY4.8: 11 residues within 4Å: Chain A: A.40, G.43, L.44, K.47, Y.48, A.395, L.399, L.430, E.433, V.434, E.437 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.44, A:L.399, A:L.430, A:V.434 Hydrogen bonds: A:A.40, A:K.47, A:E.433

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 F2X-Entry library fragment D02. 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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