SMTL ID : 8cfe.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment B03

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: 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: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:D.234, A:G.236, A:F.327, A:E.330 NAD.8: 33 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: L.449, Q.453, K.466, Y.470 Ligands: ADE.9, PO4.13 26 PLIP interactions: 20 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:N.202, 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, C:Y.470 Water bridges: B:T.169, B:N.192, B:G.236, B:F.327, B:E.330 NAD.14: 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.15, PO4.20 25 PLIP interactions: 21 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 Water bridges: C:T.169, C:N.192, C:G.236, C:F.327, C:E.330 NAD.24: 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.25, PO4.30 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.169, 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: 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, PO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:H.385 ADE.9: 13 residues within 4Å: Chain B: I.63, H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.8, PO4.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 ADE.15: 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.14, PO4.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:H.385 ADE.25: 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.24, PO4.30 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385

2 x T9G: 2-[(1R)-1-aminopropyl]phenol(Non-covalent)

T9G.3: 6 residues within 4Å: Chain A: A.40, G.43, L.44, E.433, V.434, E.437 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.44, A:L.44, A:E.433, A:V.434 Hydrogen bonds: A:A.40, A:E.437 Water bridges: A:E.437 T9G.17: 7 residues within 4Å: Chain C: A.40, G.43, L.44, K.47, E.433, V.434, E.437 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.44, C:K.47, C:E.433, C:V.434 Hydrogen bonds: C:A.40, C:E.437

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.10, H2O.24 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.8, H2O.26 K.18: 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.36, H2O.37 K.27: 4 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.52, H2O.53

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

PO4.5: 5 residues within 4Å: Chain A: K.313, L.315, K.316, K.317, R.354 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.317 Water bridges: A:K.313, A:K.317, A:K.317, A:R.354, A:R.354, A:D.366 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:R.45, A:E.74 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.64, A:D.201, A:D.201 Water bridges: A:T.168 Salt bridges: A:K.197 PO4.11: 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 Hydrogen bonds: B:E.35, B:E.35 Water bridges: B:R.45, B:R.45 Salt bridges: B:R.28, A:H.363 PO4.12: 6 residues within 4Å: Chain B: K.313, A.314, L.315, K.316, K.317, R.354 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.314, B:L.315 Water bridges: B:K.317, B:K.317 Salt bridges: B:R.354 PO4.13: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.167, B:T.168 Salt bridges: B:K.197 PO4.19: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.35 Water bridges: C:R.45, C:R.45, D:H.363 Salt bridges: C:R.28, D:H.363 PO4.20: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.14, ADE.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.64, C:E.167, C:T.168, C:D.201 Salt bridges: C:K.197 PO4.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.22: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.465 PO4.23: 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:A.314, C:L.315, C:K.317 Salt bridges: C:R.354 PO4.28: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.317 Water bridges: D:K.313, D:R.354, D:R.354, D:D.366 Salt bridges: D:R.354 PO4.29: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Water bridges: D:R.45, D:R.45, D:R.45 Salt bridges: D:R.28, C:H.363 PO4.30: 10 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.24, ADE.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.64, D:T.168, D:D.201 Salt bridges: D:K.197 PO4.31: 6 residues within 4Å: Chain D: G.458, V.459, P.464, F.465, K.466, P.467 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.458 Water bridges: D:G.458, D:F.465

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

DMS.16: 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) DMS.26: 8 residues within 4Å: Chain A: D.468, T.469, Y.470, R.471 Chain D: D.468, T.469, Y.470, R.471 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.470

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 B03. 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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