SMTL ID : 8ajv.2 (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

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

PO4.1: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.363, A:R.28 Water bridges: A:R.45 PO4.2: 6 residues within 4Å: Chain A: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142 Water bridges: A:T.168 Salt bridges: A:H.64, A:H.326 PO4.3: 7 residues within 4Å: Chain A: K.203, K.237, Q.262, D.266 Chain D: K.203, Y.204, R.207 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:Q.262, D:Y.204, D:Y.204, D:Y.204, D:R.207 Salt bridges: A:K.203, D:K.203 Water bridges: D:K.203, D:K.203 PO4.5: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 8 PLIP interactions: 7 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, B:R.45, B:R.45 Salt bridges: B:R.28, A:H.363 PO4.6: 6 residues within 4Å: Chain B: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.142, B:T.168 Salt bridges: B:H.64, B:H.326 PO4.7: 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: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Y.204, C:R.207, B:Q.262, B:D.266 Water bridges: C:K.203, C:K.203, C:R.207 Salt bridges: C:K.203, B:K.203 PO4.8: 8 residues within 4Å: Chain B: K.199, K.203, Y.204, R.207 Chain C: K.203, K.237, Q.262, D.266 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Q.262, B:Y.204, B:R.207 Water bridges: C:K.203, C:K.203 Salt bridges: C:K.203, B:K.199, B:K.203 PO4.11: 5 residues within 4Å: Chain C: R.28, I.32, E.35, E.74 Chain D: H.363 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.35, C:E.74 Water bridges: C:R.28, C:R.45, C:R.45, D:H.363 Salt bridges: C:R.28, D:H.363 PO4.12: 6 residues within 4Å: Chain C: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.168, C:T.168, C:T.168 Water bridges: C:H.64 Salt bridges: C:H.64, C:H.326 PO4.15: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Water bridges: D:R.45, D:R.45 Salt bridges: D:R.28, C:H.363 PO4.16: 6 residues within 4Å: Chain D: H.64, D.142, T.168, H.326, L.376 Ligands: NAD.18 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.142, D:T.168 Water bridges: D:H.64 Salt bridges: D:H.64, D:H.326 PO4.17: 8 residues within 4Å: Chain A: K.199, K.203, Y.204, R.207 Chain D: K.203, K.237, Q.262, D.266 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:Y.204, D:Q.262, D:D.266, D:D.266 Water bridges: A:K.203, D:K.203 Salt bridges: A:K.199, A:K.203, A:R.207, D:K.203

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

NAD.4: 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: PO4.2 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:G.233, A:D.234, A:G.236, A:F.327, A:E.330 NAD.9: 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: PO4.6 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.170, 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:I.324, B:H.326, B:N.378, C:Q.453, C:Q.453, C:K.466, C:K.466 Water bridges: B:N.192, B:G.233, B:D.234, B:G.236, B:F.327, B:E.330 NAD.13: 30 residues within 4Å: Chain B: 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: PO4.12 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:N.202, C:V.235 Hydrogen bonds: C:T.169, C:T.169, 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:N.192, C:N.192, C:G.236, C:G.325, C:F.327 NAD.18: 31 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: PO4.16 26 PLIP interactions: 6 interactions with chain A, 20 interactions with chain D Hydrogen bonds: A:Q.453, A:K.466, A:K.466, A:Y.470, A:Y.470, D:T.169, D:T.169, 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 Water bridges: A:Q.453, D:N.192, D:G.233, D:G.236, D:F.327, D:E.330 Hydrophobic interactions: D:N.202, D:V.235

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: W.342, E.343, E.344, F.360 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.344 GOL.14: 9 residues within 4Å: Chain C: T.66, I.67, N.68, Q.94, T.383, H.385, P.386, S.387 Chain D: D.219 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.66, C:I.67, C:N.68, C:N.68, C:H.385, C:S.387 Water bridges: C:E.30, C:S.387 GOL.19: 3 residues within 4Å: Chain D: K.112, P.347, Q.348 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.348 Water bridges: D:D.95, D:K.112, D:K.112, D:P.347 GOL.20: 9 residues within 4Å: Chain C: D.219 Chain D: T.66, I.67, N.68, Q.94, T.383, H.385, P.386, S.387 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.67, D:N.68, D:N.68, D:Q.94, D:S.387, D:S.387

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
FFF

B
GGG

C
HHH

D
III

Adenosylhomocysteinase

Related Entries With Identical Sequence