SMTL ID : 8ajv.1 (1 other biounit)

Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized in the presence of K+ cations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 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: PO4.4 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.169, A:T.170, A:T.170, A:N.202, 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.233, A:G.236, A:F.327, A:E.330 NAD.6: 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, L.376, N.378, H.385 Chain C: Q.453, K.466, Y.470 Ligands: PO4.11 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.170, B:T.170, B:N.202, 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:K.466, C:K.466, C:Y.470 Water bridges: B:T.169, B:N.192, B:G.233, B:G.236, B:F.327, B:E.330, C:T.447, C:Q.453 NAD.15: 31 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: PO4.18 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:N.202, C:V.235 Hydrogen bonds: C:T.169, C:T.169, C:T.170, C:T.170, C:N.202, 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:K.466, B:K.466 Water bridges: C:G.233, C:D.234, C:D.234, C:G.236, C:F.327, C:E.330, B:Q.453 NAD.21: 30 residues within 4Å: Chain A: 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: PO4.26 23 PLIP interactions: 5 interactions with chain A, 18 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: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 Hydrophobic interactions: D:V.235 Water bridges: D:G.236, D:F.327, D:E.330

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.169, T.170, H.173, G.302 Chain D: Y.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.170 GOL.7: 5 residues within 4Å: Chain B: R.337, W.342, H.350, E.373 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.337, B:R.337, B:E.373 GOL.8: 10 residues within 4Å: Chain A: E.37, R.388 Chain B: H.220, K.225, I.294, D.295, K.316, K.317, R.318, A.319 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:E.37, A:R.388, B:K.225, B:K.316, B:K.317 Water bridges: B:H.220, B:H.220, B:H.220, B:K.225, B:V.320 GOL.9: 4 residues within 4Å: Chain B: W.342, E.343, E.344 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.344, B:E.344 GOL.16: 5 residues within 4Å: Chain C: K.17, A.19, W.111, E.118 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.17 GOL.22: 7 residues within 4Å: Chain A: R.471 Chain D: V.425, L.426, P.427, K.428, D.431, D.468 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:L.426, D:K.428, D:D.431, D:D.468, A:R.471 Water bridges: D:K.428 GOL.23: 2 residues within 4Å: Chain D: K.357, D.358 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.357, D:D.358 GOL.24: 6 residues within 4Å: Chain A: Q.245 Chain B: Q.245, E.246, G.247 Chain D: R.244, D.266 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Water bridges: A:R.207, A:Q.241, A:Q.241, D:R.244 Hydrogen bonds: D:R.244

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

PO4.3: 5 residues within 4Å: Chain A: R.28, I.32, E.35, E.74 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:R.45 PO4.4: 6 residues within 4Å: Chain A: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.142, A:T.168 Water bridges: A:H.64 Salt bridges: A:H.64, A:H.326 PO4.5: 8 residues within 4Å: Chain A: K.203, K.237, Q.262, D.266 Chain D: K.199, K.203, Y.204, R.207 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:Q.262, A:D.266, A:D.266, D:Y.204, D:R.207 Water bridges: A:K.203, D:K.203 Salt bridges: A:K.203, D:K.203 PO4.10: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.45, B:R.45, B:E.74 Salt bridges: B:R.28, A:H.363 PO4.11: 6 residues within 4Å: Chain B: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.168 Salt bridges: B:H.64, B:H.326 PO4.12: 7 residues within 4Å: Chain B: K.199, K.203, Y.204 Chain C: K.203, K.237, Q.262, D.266 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.204, B:Y.204, C:Q.262 Water bridges: B:K.203, B:K.203, B:K.203, B:K.203 Salt bridges: B:K.199, B:K.203, C:K.203 PO4.13: 7 residues within 4Å: Chain B: K.203, K.237, Q.262, D.266 Chain C: K.203, Y.204, R.207 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Y.204, C:R.207, B:Q.262 Water bridges: C:K.203, B:K.203, B:K.203, B:K.203 Salt bridges: C:K.203, B:K.203 PO4.17: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.35 Water bridges: C:E.35, C:R.45 Salt bridges: C:R.28, D:H.363 PO4.18: 7 residues within 4Å: Chain C: H.64, D.142, T.168, H.326, L.376, L.379 Ligands: NAD.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.142, C:T.168 Water bridges: C:H.64, C:T.168, C:D.201 Salt bridges: C:H.64, C:H.326 PO4.25: 5 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35, E.74 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Water bridges: D:R.28, D:R.45, D:R.45, D:R.45 Salt bridges: D:R.28, C:H.363 PO4.26: 6 residues within 4Å: Chain D: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.142 Salt bridges: D:H.64, D:H.326 PO4.27: 7 residues within 4Å: Chain A: K.203, Y.204, R.207 Chain D: K.203, K.237, Q.262, D.266 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:Q.262, A:Y.204, A:Y.204, A:Y.204 Salt bridges: D:K.203, A:K.203, A:R.207 Water bridges: A:K.203, A:K.203

1 x K: POTASSIUM ION(Non-covalent)

K.14: 3 residues within 4Å: Chain B: R.337, W.340, K.357 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:R.337, B:W.340

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 9 residues within 4Å: Chain C: E.30, I.33, A.34, I.67, N.68, H.385, P.386, S.387 Chain D: D.219 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.34, C:N.68, C:S.387, D:D.219, D:D.219 Water bridges: C:I.67, C:S.387, D:T.218, D:H.220 PEG.20: 5 residues within 4Å: Chain C: K.17, E.117, E.118, W.121 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.117, C:E.117, C:E.118, C:E.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drozdzal, P. et al., Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized in the presence of K+ cations. To Be Published

Release Date

2023-08-16

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Adenosylhomocysteinase

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