SMTL ID : 8cfy.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H08

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-octamer

Ligands

8 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, PO4.6 24 PLIP interactions: 18 interactions with chain A, 6 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, D:Y.470 Water bridges: A:N.192, A:G.236, A:F.327, A:E.330 NAD.7: 30 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, N.378, H.385 Chain C: Q.453, K.466, Y.470 Ligands: ADE.8, PO4.13 26 PLIP interactions: 20 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.235 Hydrogen bonds: B:T.169, B:T.169, B:T.169, 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, PO4.19 26 PLIP interactions: 4 interactions with chain B, 22 interactions with chain C Hydrogen bonds: B:Q.453, B:Q.453, B:K.466, B:K.466, 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 Hydrophobic interactions: C:N.202, C:V.235 Water bridges: C:D.234, C:D.234, C:G.236, C:F.327, C:E.330 NAD.21: 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.22, PO4.27 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.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 NAD.28: 32 residues within 4Å: Chain E: 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 H: L.449, Q.453, K.466, Y.470 Ligands: ADE.29, PO4.35 26 PLIP interactions: 21 interactions with chain E, 5 interactions with chain H Hydrophobic interactions: E:V.235 Hydrogen bonds: E:T.169, E:T.169, E:T.170, E:T.170, E:T.170, E:N.202, E:G.233, E:D.234, E:V.235, E:V.255, E:D.256, E:N.303, E:H.326, E:N.378, E:N.378, H:Q.453, H:Q.453, H:K.466, H:K.466, H:Y.470 Water bridges: E:N.192, E:D.234, E:G.236, E:F.327, E:E.330 NAD.36: 31 residues within 4Å: Chain F: 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 Chain G: L.449, Q.453, K.466, Y.470 Ligands: ADE.37, PO4.42 27 PLIP interactions: 21 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:V.235 Hydrogen bonds: F:T.169, F:T.169, F:T.169, F:T.170, F:T.170, F:N.202, F:G.233, F:D.234, F:V.235, F:V.255, F:D.256, F:N.303, F:H.326, F:N.378, F:N.378, G:Q.453, G:Q.453, G:K.466, G:K.466, G:Y.470 Water bridges: F:N.192, F:D.234, F:G.236, F:F.327, F:E.330, G:T.450 NAD.43: 32 residues within 4Å: Chain F: L.449, Q.453, K.466, Y.470 Chain G: 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.44, PO4.50 27 PLIP interactions: 20 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:V.235 Hydrogen bonds: G:T.169, G:T.169, G:T.169, G:T.170, G:N.202, G:G.233, G:D.234, G:V.235, G:V.255, G:D.256, G:N.303, G:H.326, G:N.378, G:N.378, F:Q.453, F:Q.453, F:K.466, F:K.466, F:Y.470, F:Y.470 Water bridges: G:T.169, G:N.192, G:G.236, G:F.327, G:E.330 Salt bridges: F:K.466 NAD.52: 32 residues within 4Å: Chain E: L.449, Q.453, K.466, Y.470 Chain H: 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.53, PO4.57 25 PLIP interactions: 19 interactions with chain H, 6 interactions with chain E Hydrophobic interactions: H:V.235 Hydrogen bonds: H:T.169, H:T.169, H:T.169, H:T.170, H:N.202, H:G.233, H:D.234, H:V.235, H:V.255, H:D.256, H:N.303, H:H.326, H:N.378, H:N.378, E:Q.453, E:Q.453, E:K.466, E:K.466, E:Y.470, E:Y.470 Water bridges: H:N.192, H:G.236, H:F.327, H:E.330

8 x ADE: ADENINE(Non-covalent)

ADE.2: 13 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, K.3, PO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68, A:H.385 ADE.8: 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.7, 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, PO4.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:T.69, C:H.385 ADE.22: 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.21, K.24, PO4.27 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385 ADE.29: 12 residues within 4Å: Chain E: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.28, PO4.35 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.66, E:Q.68, E:T.69, E:H.385 ADE.37: 12 residues within 4Å: Chain F: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.36, PO4.42 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.66, F:Q.68, F:T.69, F:H.385 ADE.44: 12 residues within 4Å: Chain G: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.43, PO4.50 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.68, G:H.385 ADE.53: 12 residues within 4Å: Chain H: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.52, PO4.57 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.68, H:H.385

8 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385, P.386 Ligands: ADE.2 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.7 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.21, H2O.22 K.17: 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.35, H2O.37 K.24: 6 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385, P.386 Ligands: ADE.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.48, H2O.51 K.30: 5 residues within 4Å: Chain E: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.383, E:T.383, E:H.385, H2O.62, H2O.64 K.40: 5 residues within 4Å: Chain F: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.383, F:T.383, F:H.385, H2O.62, H2O.75 K.47: 4 residues within 4Å: Chain G: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.383, G:T.383, G:H.385, H2O.90, H2O.93 K.55: 4 residues within 4Å: Chain H: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:T.383, H:T.383, H:H.385, H2O.104, H2O.105

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

PO4.4: 5 residues within 4Å: Chain A: K.313, A.314, L.315, K.317, R.354 Ligand excluded by PLIP PO4.5: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 Ligand excluded by PLIP PO4.6: 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 Ligand excluded by PLIP PO4.11: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 Ligand excluded by PLIP PO4.12: 6 residues within 4Å: Chain B: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP 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.7, ADE.8 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 Ligand excluded by PLIP PO4.19: 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 Ligand excluded by PLIP PO4.20: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.25: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.26: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 Ligand excluded by PLIP PO4.27: 10 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.21, ADE.22 Ligand excluded by PLIP PO4.31: 6 residues within 4Å: Chain E: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.32: 4 residues within 4Å: Chain E: H.363 Chain F: R.28, I.32, E.35 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain E: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.34: 4 residues within 4Å: Chain E: R.28, I.32, E.35 Chain F: H.363 Ligand excluded by PLIP PO4.35: 10 residues within 4Å: Chain E: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.28, ADE.29 Ligand excluded by PLIP PO4.41: 6 residues within 4Å: Chain F: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.42: 10 residues within 4Å: Chain F: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.36, ADE.37 Ligand excluded by PLIP PO4.48: 4 residues within 4Å: Chain G: R.28, I.32, E.35 Chain H: H.363 Ligand excluded by PLIP PO4.49: 4 residues within 4Å: Chain G: H.363 Chain H: R.28, I.32, E.35 Ligand excluded by PLIP PO4.50: 10 residues within 4Å: Chain G: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.43, ADE.44 Ligand excluded by PLIP PO4.51: 6 residues within 4Å: Chain G: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.56: 6 residues within 4Å: Chain H: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.57: 10 residues within 4Å: Chain H: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.52, ADE.53 Ligand excluded by PLIP PO4.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

DMS.9: 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.16: 5 residues within 4Å: Chain C: K.313, A.314, L.315, K.317, R.354 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.354, C:R.354 DMS.23: 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.45: 5 residues within 4Å: Chain G: K.313, A.314, L.315, K.317, R.354 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.354 Salt bridges: G:D.366 DMS.46: 7 residues within 4Å: Chain F: D.468, T.469, R.471 Chain G: D.468, T.469, Y.470, R.471 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.471 DMS.54: 8 residues within 4Å: Chain E: D.468, T.469, Y.470, R.471 Chain H: D.468, T.469, Y.470, R.471 1 PLIP interactions: 1 interactions with chain E Water bridges: E:R.471

2 x UIV: ~{N}-methyl-~{N}-[(1-methylpyrazol-4-yl)methyl]cyclohexanecarboxamide(Non-covalent)

UIV.38: 2 residues within 4Å: Chain F: N.279 Chain G: P.451 No protein-ligand interaction detected (PLIP) UIV.39: 8 residues within 4Å: Chain F: A.40, G.43, L.44, K.47, Y.48, K.429, E.433, E.437 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.44, F:E.433, F:E.437

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 H08. To be published

Release Date

2024-02-21

Peptides

Adenosylhomocysteinase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
H

G
I

H
J

Adenosylhomocysteinase

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