SMTL ID : 3mqh.1 (1 other biounit)

crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with CoA and UDP-3-amino-2-acetamido-2,3-dideoxy glucuronic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-trimer

Ligands

3 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: 20 residues within 4Å: Chain A: W.25, H.26, S.41, Q.44, K.59, Q.61, N.62, F.77 Chain C: H.29, F.47, Y.67, N.86, V.87, P.90, E.95, R.96, K.97, Y.100 Ligands: COA.10, EDO.14 28 PLIP interactions: 16 interactions with chain A, 12 interactions with chain C Hydrogen bonds: A:S.41, A:Q.44, A:Q.61, A:Q.61, A:N.62, C:N.86, C:R.96, C:Y.100 Water bridges: A:R.23, A:R.23, A:H.26, A:K.59, A:K.59, A:I.60, A:Q.61, C:H.29, C:N.50, C:N.50, C:D.68, C:K.97 Salt bridges: A:K.59, A:K.59, A:K.59, C:K.97, C:K.97, C:K.97 pi-Stacking: A:W.25 Hydrophobic interactions: C:Y.67 MJZ.6: 22 residues within 4Å: Chain A: H.29, C.31, F.47, Y.67, N.86, V.87, P.90, I.94, E.95, R.96, K.97, Y.100 Chain B: W.25, H.26, S.41, Q.44, K.59, Q.61, N.62, F.77 Ligands: COA.2, EDO.3 29 PLIP interactions: 13 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:S.41, B:Q.44, B:Q.61, B:Q.61, B:N.62, A:N.86, A:R.96, A:K.97, A:Y.100 Water bridges: B:R.23, B:H.26, B:K.59, B:K.59, B:Q.61, A:H.29, A:N.50, A:N.50, A:K.97, A:K.97, A:K.97, A:K.97, A:K.97, A:K.97 Salt bridges: B:K.59, B:K.59, A:K.97, A:K.97 pi-Stacking: B:W.25 Hydrophobic interactions: A:Y.67 MJZ.11: 21 residues within 4Å: Chain B: H.29, F.47, Y.67, N.86, V.87, P.90, I.94, E.95, R.96, K.97, Y.100 Chain C: W.25, H.26, S.41, Q.44, K.59, Q.61, N.62, F.77 Ligands: COA.7, EDO.8 28 PLIP interactions: 12 interactions with chain B, 16 interactions with chain C Hydrophobic interactions: B:Y.67 Hydrogen bonds: B:N.86, B:R.96, B:Y.100, C:S.41, C:Q.44, C:Q.61, C:Q.61, C:N.62 Water bridges: B:H.29, B:N.50, B:K.97, B:K.97, B:K.97, B:K.97, C:R.23, C:R.23, C:H.26, C:K.59, C:K.59, C:I.60, C:Q.61 Salt bridges: B:K.97, B:K.97, C:K.59, C:K.59, C:K.59 pi-Stacking: C:W.25

3 x COA: COENZYME A(Non-covalent)

COA.2: 20 residues within 4Å: Chain A: T.85, N.86, V.87, Y.88, P.90, N.136, P.149, R.151 Chain B: F.77, P.80, G.112, A.113, F.128, G.130, A.131, L.144, V.146, I.153, Q.162 Ligands: MJZ.6 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.128, B:L.144, A:Y.88 Hydrogen bonds: B:A.113, B:A.131, B:A.131, B:Q.162, A:V.87, A:Y.88, A:Y.88, A:N.136, A:N.136, A:R.151 Water bridges: B:G.147, A:Y.88, A:Y.88 Salt bridges: A:R.151 COA.7: 20 residues within 4Å: Chain B: T.85, N.86, V.87, Y.88, P.90, V.134, N.136, P.149, R.151 Chain C: F.77, P.80, G.112, A.113, F.128, G.130, A.131, V.146, I.153, Q.162 Ligands: MJZ.11 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:Y.88, C:F.128 Hydrogen bonds: B:V.87, B:Y.88, B:Y.88, B:N.136, B:R.151, C:A.113, C:A.131, C:A.131, C:Q.162 Water bridges: B:Y.88, B:Y.88, B:R.151, C:G.147 COA.10: 22 residues within 4Å: Chain A: F.77, P.80, G.112, A.113, F.128, G.130, A.131, L.144, V.146, I.153, Q.162 Chain C: T.85, N.86, V.87, Y.88, P.90, V.134, N.136, V.148, P.149, R.151 Ligands: MJZ.1 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:F.128, A:L.144 Hydrogen bonds: A:A.113, A:A.131, A:A.131, A:Q.162, C:V.87, C:Y.88, C:Y.88, C:N.136, C:N.136, C:R.151 Water bridges: A:G.147, C:Y.88, C:R.151, C:R.151

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

EDO.3: 4 residues within 4Å: Chain A: F.47, G.49, D.68 Ligands: MJZ.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.50 Water bridges: A:N.50, A:N.86 EDO.5: 5 residues within 4Å: Chain A: T.5, H.7, R.23, I.24, W.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.5 Water bridges: A:I.6 EDO.8: 5 residues within 4Å: Chain B: F.47, G.49, N.50, D.68 Ligands: MJZ.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.50 Water bridges: B:N.50, B:N.86 EDO.9: 7 residues within 4Å: Chain B: V.134, V.135, N.136, K.137, D.138, V.139, A.150 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.134, B:N.136, B:K.137, B:D.138, B:A.150 Water bridges: B:N.136 EDO.13: 6 residues within 4Å: Chain C: R.17, G.19, E.35, I.36, G.37 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.17, C:R.17 EDO.14: 4 residues within 4Å: Chain C: F.47, G.49, D.68 Ligands: MJZ.1 5 PLIP interactions: 5 interactions with chain C Water bridges: C:N.50, C:D.68, C:N.86, C:K.97, C:K.97 EDO.15: 3 residues within 4Å: Chain C: G.37, N.56 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.56

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

NA.4: 3 residues within 4Å: Chain A: N.114 Chain B: N.114 Chain C: N.114 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:N.114, B:N.114, C:N.114, A:N.114

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

PO4.12: 7 residues within 4Å: Chain A: N.114, G.132, V.148 Chain B: N.114, G.132 Chain C: N.114, G.132 8 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:G.132, B:G.132 Water bridges: A:N.114, B:N.114, B:N.114, B:T.116, C:N.114, C:T.116

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.16: 7 residues within 4Å: Chain C: E.35, R.53, F.71, L.72, E.73, I.104, R.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.53

Links

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Citation

Thoden, J.B. et al., Molecular structure of WlbB, a bacterial N-acetyltransferase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid . Biochemistry (2010)

Release Date

2010-05-12

Peptides

Lipopolysaccharides biosynthesis acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Lipopolysaccharides biosynthesis acetyltransferase

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