SMTL ID : 7l7x.1

X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 17 residues within 4Å: Chain A: N.62, G.63, T.64, L.67, T.88, F.89, A.91, S.92, V.134, D.160, A.162, Q.163, S.184, C.186, K.189 Chain B: N.243 Ligands: 4RA.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.89, A:V.134, A:A.162 Hydrogen bonds: A:G.63, A:T.64, A:T.64, A:Q.163, A:S.184, A:S.184, A:K.189, A:G.197, B:N.243 Water bridges: B:R.245, B:R.245 PMP.11: 17 residues within 4Å: Chain A: N.243 Chain B: N.62, G.63, T.64, L.67, T.88, F.89, A.91, S.92, V.134, D.160, A.162, Q.163, S.184, C.186, K.189 Ligands: 4RA.12 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.89, B:V.134 Hydrogen bonds: B:G.63, B:T.64, B:T.64, B:Q.163, B:S.184, B:S.184, B:S.184, B:K.189, A:N.243 Water bridges: A:R.245, A:R.245

2 x 4RA: [(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate(Non-covalent)

4RA.2: 27 residues within 4Å: Chain A: N.62, G.63, T.64, T.88, F.89, A.91, S.92, V.134, D.160, A.162, Q.163, S.184, C.186, Q.187, K.189, F.339, S.340, G.341 Chain B: N.34, K.219, G.232, Y.233, R.234, L.236, N.243, R.245 Ligands: PMP.1 28 PLIP interactions: 18 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.89, A:F.89, A:V.134 Hydrogen bonds: A:N.62, A:G.63, A:T.64, A:T.64, A:Q.163, A:S.184, A:S.184, A:Q.187, A:K.189, A:S.340, A:G.341, B:Y.233, B:Y.233, B:R.234, B:N.243 Water bridges: A:D.188, A:S.340, A:A.343, A:A.343, B:K.219, B:K.219, B:R.234, B:R.245, B:R.245 Salt bridges: B:K.219 4RA.12: 28 residues within 4Å: Chain A: N.34, K.219, G.232, Y.233, R.234, L.236, N.243, R.245 Chain B: N.62, G.63, T.64, L.67, T.88, F.89, A.91, S.92, V.134, D.160, A.162, Q.163, S.184, C.186, Q.187, K.189, F.339, S.340, G.341 Ligands: PMP.11 28 PLIP interactions: 18 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.89, B:F.89, B:V.134, A:Y.233 Hydrogen bonds: B:G.63, B:T.64, B:T.64, B:Q.163, B:S.184, B:S.184, B:Q.187, B:K.189, B:S.340, B:G.341, A:Y.233, A:R.234, A:N.243 Water bridges: B:D.188, B:Y.307, B:S.340, B:A.343, B:A.343, A:K.219, A:K.219, A:R.234, A:R.245, A:R.245 Salt bridges: A:K.219

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: D.80, K.129 Ligands: NA.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.80 Water bridges: A:G.77, A:K.129 EDO.4: 4 residues within 4Å: Chain A: A.270, N.271, T.274, I.387 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.274 EDO.5: 3 residues within 4Å: Chain A: Q.206, R.209, K.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.206, A:K.210 Water bridges: A:R.209 EDO.6: 3 residues within 4Å: Chain A: D.151, K.152, N.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.154, A:N.154 EDO.7: 6 residues within 4Å: Chain A: F.352, N.354, T.355, G.356, L.357, R.358 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.354, A:T.355, A:G.356, A:R.358, A:R.358 Water bridges: A:N.354, A:R.358 EDO.13: 3 residues within 4Å: Chain B: Q.18, I.19, D.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.22 Water bridges: B:D.22, B:D.22 EDO.14: 3 residues within 4Å: Chain A: W.244 Chain B: N.98, W.244 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:W.244 Hydrogen bonds: B:N.98 EDO.15: 2 residues within 4Å: Chain B: I.177, H.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.177 Water bridges: B:N.203, B:N.203 EDO.16: 4 residues within 4Å: Chain B: I.19, I.256, K.259, R.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.260 EDO.17: 3 residues within 4Å: Chain B: A.280, R.292, E.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.292, B:E.295

2 x TMA: TETRAMETHYLAMMONIUM ION(Non-covalent)

TMA.8: 4 residues within 4Å: Chain A: W.51, D.53, T.168, S.173 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.53 pi-Cation interactions: A:W.51 TMA.18: 4 residues within 4Å: Chain B: W.51, D.53, T.168, S.173 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.53 pi-Cation interactions: B:W.51

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain A: D.126, T.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.126 NA.10: 2 residues within 4Å: Chain A: K.129 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linehan, M.P. et al., Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar. J.Biol.Chem. (2021)

Release Date

2021-03-03

Peptides

DegT/DnrJ/EryC1/StrS aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

DegT/DnrJ/EryC1/StrS aminotransferase