SMTL ID : 2iu9.1

Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-trimer

Ligands

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 6 residues within 4Å: Chain A: R.188, C.208, H.222 Chain B: H.182, I.198, Q.200 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.188, A:R.188, B:Q.200

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: S.84, R.85, T.86, T.101, S.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.85, A:T.86, A:T.86, A:T.101 Salt bridges: A:R.85 SO4.3: 6 residues within 4Å: Chain A: L.262, Q.280 Chain B: L.262, Q.280 Chain C: L.262, Q.280 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Q.280, A:Q.280, A:Q.280, B:Q.280 SO4.5: 5 residues within 4Å: Chain B: S.84, R.85, T.86, T.101, S.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.84, B:R.85, B:T.86, B:T.86 Salt bridges: B:R.85 SO4.8: 1 residues within 4Å: Chain A: H.310 No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain C: R.85, S.102 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.85, C:I.100, C:S.102, C:S.102 Salt bridges: C:R.85 SO4.10: 6 residues within 4Å: Chain A: H.182, Q.200 Chain C: R.188, C.208, H.222, K.224 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Q.200 Salt bridges: A:H.182, C:R.188, C:H.222, C:K.224 Water bridges: C:K.224

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 18 residues within 4Å: Chain A: Q.264, A.266, G.282, I.283, A.284, G.300, I.301, T.302, V.319, T.320 Chain B: D.260, V.278, A.279, Q.280, G.297, M.314, A.315, Q.316 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.264, A:A.284, B:V.278, B:M.314 Hydrogen bonds: A:Q.264 PLM.7: 16 residues within 4Å: Chain B: Q.264, A.266, G.282, I.283, A.284, G.300, I.301, T.302, G.318, T.320, A.332 Chain C: D.260, V.278, A.279, A.315, Q.316 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.279, C:A.315, C:Q.316, C:Q.316, B:Q.264, B:A.266, B:T.320, B:A.332 Hydrogen bonds: C:D.260, B:Q.264 PLM.12: 16 residues within 4Å: Chain A: D.260, V.278, A.279, I.294, I.312, M.313, M.314, A.315 Chain C: Q.264, A.266, G.282, I.283, A.284, G.300, I.301, T.302 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.278, A:A.279, A:I.294, A:I.312, A:A.315, A:A.315, C:Q.264, C:T.302 Hydrogen bonds: C:Q.264

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

UD1.6: 13 residues within 4Å: Chain A: H.267, Q.268, S.286, H.304 Chain B: E.52, I.53, E.54, T.62, F.63, L.64, D.65, N.66, Y.69 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.66 Hydrogen bonds: B:E.52, B:I.53, B:E.54, B:T.62, B:F.63, B:D.65, B:N.66, B:N.66, A:Q.268, A:S.286 pi-Stacking: B:F.63, B:Y.69 Salt bridges: A:H.304, A:H.304 UD1.11: 17 residues within 4Å: Chain B: G.211, Y.212, F.248, H.267, Q.268, G.285, S.286, G.303, H.304 Chain C: E.52, I.53, E.54, T.62, F.63, L.64, D.65, Y.69 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:Y.212, B:H.267, B:Q.268, B:S.286, B:H.304, C:E.52, C:I.53, C:E.54, C:T.62, C:F.63, C:D.65, C:Y.69, C:Y.69 Salt bridges: B:H.304, B:H.304 Hydrophobic interactions: C:Y.69 pi-Stacking: C:F.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buetow, L. et al., Structure and Reactivity of Lpxd, the N-Acyltransferase of Lipid a Biosynthesis. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-02-20

Peptides

UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE

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