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

crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with acetyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-trimer

Ligands

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 21 residues within 4Å: Chain A: Y.67, T.85, N.86, V.87, Y.88, P.90, N.136, P.149, R.151 Chain B: Q.61, F.77, P.80, G.112, A.113, F.128, G.130, A.131, L.144, V.146, I.153, Q.162 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:P.80, B:F.128, B:L.144, A:Y.67 Hydrogen bonds: B:A.113, B:A.131, B:A.131, B:Q.162, A:N.86, A:V.87, A:V.87, A:Y.88, A:Y.88, A:N.136, A:N.136 Water bridges: B:G.147, A:Y.88, A:Y.88, A:Y.88 Salt bridges: A:R.151 ACO.4: 21 residues within 4Å: Chain B: Y.67, T.85, N.86, V.87, Y.88, P.90, N.136, P.149 Chain C: Q.61, F.77, P.80, G.112, A.113, F.128, G.130, A.131, L.144, V.146, I.153, M.156, Q.162 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:Y.67, C:P.80, C:F.128, C:L.144 Hydrogen bonds: B:N.86, B:V.87, B:V.87, B:Y.88, B:Y.88, B:N.136, B:N.136, C:A.113, C:A.131, C:A.131, C:Q.162 Water bridges: B:Y.88, B:Y.88, B:Y.88, B:K.137, C:G.147 ACO.8: 22 residues within 4Å: Chain A: Q.61, F.77, P.80, G.112, A.113, F.128, G.130, A.131, L.144, V.146, I.153, Q.162 Chain C: Y.67, T.85, N.86, V.87, Y.88, P.90, N.136, V.148, P.149, R.151 21 PLIP interactions: 8 interactions with chain A, 13 interactions with chain C Hydrophobic interactions: A:P.80, A:F.128, A:L.144, C:Y.67 Hydrogen bonds: A:A.113, A:A.131, A:A.131, A:Q.162, C:N.86, C:V.87, C:V.87, C:Y.88, C:Y.88, C:N.136 Water bridges: A:G.147, C:Y.88, C:Y.88, C:Y.88, C:R.151, C:R.151 Salt bridges: C:R.151

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.2: 11 residues within 4Å: Chain A: W.25, H.26, S.41, G.43, Q.44, K.59, Q.61, N.62 Chain C: H.29, F.47, Y.67 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.41, A:S.41, A:Q.44, A:Q.61, A:N.62 Water bridges: A:R.23, A:H.26, C:N.50 Salt bridges: A:K.59 pi-Stacking: A:W.25

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

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

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.5: 12 residues within 4Å: Chain A: H.29, F.47, Y.67 Chain B: R.23, W.25, H.26, S.41, G.43, Q.44, K.59, Q.61, N.62 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.41, B:S.41, B:Q.44, B:Q.61, B:N.62 Water bridges: B:H.26, B:H.26, A:H.29, A:N.50, A:K.97, A:K.97 Salt bridges: B:R.23, B:K.59, B:K.59 pi-Stacking: B:W.25 UDP.9: 12 residues within 4Å: Chain B: H.29, F.47, Y.67, K.97 Chain C: R.23, W.25, H.26, S.41, G.43, Q.44, Q.61, N.62 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Water bridges: B:N.50, C:H.26 Salt bridges: B:K.97, B:K.97, C:R.23 Hydrogen bonds: C:S.41, C:S.41, C:Q.44, C:Q.61, C:N.62 pi-Stacking: C:W.25

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

PO4.6: 8 residues within 4Å: Chain A: N.114, G.132, V.148 Chain B: N.114, G.132, V.148 Chain C: N.114, G.132 8 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:G.132, B:G.132 Water bridges: C:N.114, C:N.114, A:N.114, B:N.114, B:N.114, B:T.116

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

EDO.7: 7 residues within 4Å: Chain B: V.134, V.135, N.136, K.137, D.138, V.139, A.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.136, B:N.136, B:K.137, B:A.150 Water bridges: B:N.136 EDO.11: 2 residues within 4Å: Chain C: G.37, N.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.38, C:N.56

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

PE4.10: 6 residues within 4Å: Chain C: E.35, R.53, F.71, L.72, E.73, I.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.53 Water bridges: C:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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