SMTL ID : 4r37.1 (1 other biounit)

Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 with UDP-GlcNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.1: 19 residues within 4Å: Chain A: Q.87, D.88, L.89, K.90, H.138, G.156, H.173, Q.174, F.175 Chain B: L.129, M.131, I.147, I.165, M.183, N.211, I.213, G.214, R.217 Ligands: ACT.4 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.89, B:L.129, B:I.147 Hydrogen bonds: A:L.89, A:K.90, A:H.138, A:H.173, A:Q.174, B:N.211, B:N.211, B:G.214 Water bridges: A:D.88, B:I.213, B:R.217, B:R.217 Salt bridges: A:K.90, B:R.217, B:R.217 UD1.7: 19 residues within 4Å: Chain B: Q.87, D.88, L.89, K.90, H.138, G.156, H.173, Q.174, F.175 Chain C: L.129, M.131, I.147, I.165, M.183, N.211, I.213, G.214, R.217 Ligands: ACT.10 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:L.129, C:I.147, B:L.89 Hydrogen bonds: C:N.211, C:N.211, C:G.214, B:D.88, B:L.89, B:K.90, B:H.138, B:H.173, B:Q.174 Water bridges: C:I.213, C:R.217, C:R.217, B:D.88 Salt bridges: C:R.217, C:R.217, B:K.90 UD1.13: 19 residues within 4Å: Chain A: L.129, M.131, I.147, I.165, M.183, N.211, I.213, G.214, R.217 Chain C: Q.87, D.88, L.89, K.90, H.138, G.156, H.173, Q.174, F.175 Ligands: ACT.16 18 PLIP interactions: 8 interactions with chain C, 10 interactions with chain A Hydrophobic interactions: C:L.89, A:L.129, A:I.147 Hydrogen bonds: C:L.89, C:K.90, C:H.138, C:H.173, C:Q.174, A:N.211, A:N.211, A:G.214 Water bridges: C:D.88, A:I.213, A:R.217, A:R.217 Salt bridges: C:K.90, A:R.217, A:R.217

3 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.2: 7 residues within 4Å: Chain A: N.49, R.69, E.95, S.96, T.97, G.120, R.121 No protein-ligand interaction detected (PLIP) PE5.8: 7 residues within 4Å: Chain B: N.49, R.69, E.95, S.96, T.97, G.120, R.121 No protein-ligand interaction detected (PLIP) PE5.14: 7 residues within 4Å: Chain C: N.49, R.69, E.95, S.96, T.97, G.120, R.121 No protein-ligand interaction detected (PLIP)

3 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 6 residues within 4Å: Chain A: N.103, N.127, G.145, C.146, I.147 Chain C: L.89 No protein-ligand interaction detected (PLIP) PG0.9: 6 residues within 4Å: Chain A: L.89 Chain B: N.103, N.127, G.145, C.146, I.147 No protein-ligand interaction detected (PLIP) PG0.15: 6 residues within 4Å: Chain B: L.89 Chain C: N.103, N.127, G.145, C.146, I.147 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: Q.87, N.113, H.135, A.137 Chain B: N.150 Ligands: UD1.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.137 Hydrogen bonds: A:N.113, B:N.150 Water bridges: A:H.138 Salt bridges: A:H.135 ACT.10: 6 residues within 4Å: Chain B: Q.87, N.113, H.135, A.137 Chain C: N.150 Ligands: UD1.7 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.137 Hydrogen bonds: B:N.113, C:N.150 Water bridges: B:H.138 Salt bridges: B:H.135 ACT.16: 6 residues within 4Å: Chain A: N.150 Chain C: Q.87, N.113, H.135, A.137 Ligands: UD1.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.137 Hydrogen bonds: C:N.113, A:N.150 Water bridges: C:H.138 Salt bridges: C:H.135

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 5 residues within 4Å: Chain A: N.109 Chain B: N.109 Chain C: N.109 Ligands: CA.11, CA.17 No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain A: N.109 Chain B: N.109 Chain C: N.109 Ligands: CA.5, CA.17 No protein-ligand interaction detected (PLIP) CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 5 residues within 4Å: Chain A: N.109 Chain B: N.109 Chain C: N.109 Ligands: CA.5, CA.11 No protein-ligand interaction detected (PLIP) CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, A. et al., Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA). Acta Crystallogr.,Sect.D (2015)

Release Date

2015-05-06

Peptides

Putative acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase

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