SMTL ID : 8e62.1 (1 other biounit)

STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

2 x MJZ: (2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid(Non-covalent)

MJZ.1: 17 residues within 4Å: Chain A: E.39, D.40, K.41, H.89, G.107, H.108, H.124, Q.125, R.126, K.143 Chain C: M.82, N.116, M.134, N.164, K.166, G.167 Ligands: COA.2 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:K.41 Hydrogen bonds: A:E.39, A:K.41, A:H.89, A:G.107, A:H.124, A:Q.125, A:K.143, C:N.164, C:N.164 Water bridges: A:R.126, C:N.116, C:N.116 Salt bridges: A:H.108, A:R.126, C:K.166, C:K.166 MJZ.4: 15 residues within 4Å: Chain A: M.82, M.134, N.164, K.166, G.167 Chain B: E.39, D.40, K.41, H.89, G.107, H.124, Q.125, R.126, K.143 Ligands: COA.3 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:K.41, A:K.166 Hydrogen bonds: B:E.39, B:K.41, B:H.89, B:G.107, B:H.124, B:Q.125, B:K.143, A:N.116, A:N.164, A:N.164, A:K.166 Water bridges: B:D.40, B:R.126 Salt bridges: B:H.108, B:R.126

3 x COA: COENZYME A(Non-covalent)

COA.2: 19 residues within 4Å: Chain A: H.124, Q.125, I.140, T.142, K.143, K.144, N.156, P.157 Chain C: M.82, S.100, G.118, M.119, M.134, G.136, M.137, V.154, G.155, I.161 Ligands: MJZ.1 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:Q.125, A:Q.125, C:S.100, C:M.119, C:M.137, C:M.137, C:G.155 Water bridges: A:H.124, A:T.142, A:K.143, A:K.143, A:K.143 Salt bridges: A:K.143, A:K.143 Hydrophobic interactions: C:V.154 COA.3: 18 residues within 4Å: Chain A: M.82, S.100, G.118, M.119, M.134, G.136, M.137, V.154, G.155, I.161 Chain B: Q.125, I.140, T.142, K.143, K.144, N.156, P.157 Ligands: MJZ.4 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.154 Hydrogen bonds: A:S.100, A:M.119, A:M.137, A:M.137, A:G.155, B:Q.125, B:Q.125 Water bridges: B:K.143, B:K.143 Salt bridges: B:K.143, B:K.143, B:K.144 COA.5: 15 residues within 4Å: Chain B: M.82, S.100, G.118, M.119, M.134, G.136, M.137, V.154, I.161 Chain C: Q.125, I.140, T.142, K.143, K.144, N.156 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:Q.125, C:Q.125, C:T.142, C:K.143, B:S.100, B:M.119, B:M.137, B:M.137 Water bridges: C:T.142, C:K.144, B:G.155 Salt bridges: C:K.143, C:K.143, C:K.144 Hydrophobic interactions: B:V.154

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

NA.6: 3 residues within 4Å: Chain A: N.31 Chain B: N.31 Chain C: N.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.31, C:N.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofmeister, D.L. et al., Investigation of the enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid in Psychrobacter cryohalolentis K5 T. Protein Sci. (2023)

Release Date

2022-11-23

Peptides

UDP-N-acetylglucosamine acyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

UDP-N-acetylglucosamine acyltransferase

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