SMTL ID : 8cfg.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment C04

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 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, PO4.7 26 PLIP interactions: 5 interactions with chain D, 21 interactions with chain A Hydrogen bonds: D:Q.453, D:Q.453, D:K.466, D:K.466, D:Y.470, 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:V.235 Water bridges: A:D.234, A:D.234, A:G.236, A:F.327, A:E.330 NAD.12: 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.13, PO4.18 26 PLIP interactions: 22 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.169, B:T.170, 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 Water bridges: B:D.234, B:D.234, B:G.236, B:F.327, B:E.330 NAD.23: 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.24, PO4.27 26 PLIP interactions: 19 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: 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, B:T.447 Salt bridges: B:K.466 NAD.30: 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.31, PO4.35 26 PLIP interactions: 20 interactions with chain D, 6 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

4 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.4, PO4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:T.69, A:H.385 ADE.13: 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.12, 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.24: 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.23, PO4.27 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.68, C:T.69, C:H.385 ADE.31: 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.30, PO4.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.68, D:H.385

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

DMS.3: 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)

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 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.3, 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.21, H2O.22 K.25: 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.38, H2O.39 K.33: 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.53

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

PO4.5: 7 residues within 4Å: Chain A: K.313, A.314, L.315, K.316, K.317, R.354, D.366 Ligand excluded by PLIP PO4.6: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 Ligand excluded by PLIP 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 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain A: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.17: 6 residues within 4Å: Chain B: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP 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.12, ADE.13 Ligand excluded by PLIP PO4.19: 6 residues within 4Å: Chain B: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 Ligand excluded by PLIP PO4.26: 6 residues within 4Å: Chain C: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.27: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.23, ADE.24 Ligand excluded by PLIP PO4.28: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.29: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 Ligand excluded by PLIP PO4.34: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.35: 9 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385 Ligands: NAD.30, ADE.31 Ligand excluded by PLIP PO4.36: 6 residues within 4Å: Chain D: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.37: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 Ligand excluded by PLIP

5 x R8S: 2-hydrazinyl-4-methoxypyrimidine(Non-covalent)

R8S.9: 7 residues within 4Å: Chain A: Y.16, K.17, V.18, A.19, D.20, I.21 Ligands: R8S.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.18, A:V.18, A:I.21 R8S.10: 5 residues within 4Å: Chain A: K.17, V.18, A.19, W.111 Ligands: R8S.9 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.95, A:K.112 pi-Stacking: A:W.111, A:W.111 R8S.21: 8 residues within 4Å: Chain B: K.203, Y.232, K.237, Q.262, D.266 Chain C: K.199, K.203, Y.204 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:K.199, C:K.203, C:K.203, C:Y.204, B:Q.262 Hydrophobic interactions: B:K.237 Water bridges: B:K.203, B:K.203, B:Y.204 R8S.22: 6 residues within 4Å: Chain B: D.468, T.469, R.471 Chain C: D.468, T.469, R.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.469, B:R.471 Water bridges: B:R.471, B:R.471 R8S.38: 7 residues within 4Å: Chain A: K.199, K.203, Y.204 Chain D: K.203, K.237, Q.262, D.266 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:K.199, A:K.203, A:K.203, A:Y.204, D:Q.262 Hydrophobic interactions: D:K.237 Water bridges: D:K.203, D:K.203

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: D.219, K.346 Chain B: W.26, E.30, Q.94, Q.96, R.216, T.383 7 PLIP interactions: 4 interactions with chain B, 3 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: A:D.219 GOL.14: 4 residues within 4Å: Chain B: S.460, E.462, G.463, P.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.460, B:S.460 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.32: 7 residues within 4Å: Chain C: D.219, K.346 Chain D: W.26, E.30, Q.94, Q.96, T.383 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.30, D:Q.94, D:Q.96, D:R.216, C:K.346

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 C04. 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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