SMTL ID : 2iu8.1

CHLAMYDIA TRACHOMATIS LPXD WITH 25MM UDPGLCNAC (COMPLEX I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 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 Water bridges: A:S.84 Salt bridges: A:R.85 SO4.2: 2 residues within 4Å: Chain A: P.326 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain B: S.84, R.85, T.86, T.101, S.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.85, B:T.86, B:T.86 Salt bridges: B:R.85 SO4.7: 6 residues within 4Å: Chain A: L.262, Q.280 Chain B: L.262, Q.280 Chain C: L.262, Q.280 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.280, B:Q.280, C:Q.280 Water bridges: A:Q.280, B:Q.280 SO4.10: 2 residues within 4Å: Chain C: R.85, S.102 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.85, C:R.85, C:R.85, C:R.85, C:S.102 Salt bridges: C:R.85 SO4.11: 7 residues within 4Å: Chain A: H.182, I.198, Q.200 Chain C: R.188, C.208, H.222, K.224 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.200, A:Q.200 Salt bridges: A:H.182, C:R.188, C:H.222

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 20 residues within 4Å: Chain A: Q.264, A.266, G.282, I.283, A.284, G.285, G.300, I.301, T.302, G.318, V.319, T.320 Chain B: D.260, V.278, A.279, G.297, Q.298, M.314, A.315, Q.316 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.278, B:A.279, B:Q.298, B:A.315, B:Q.316, A:Q.264 Hydrogen bonds: B:D.260, A:Q.264, A:G.285 Water bridges: A:H.267 PLM.9: 19 residues within 4Å: Chain B: Q.264, A.266, G.282, I.283, A.284, G.300, I.301, T.302, G.318, V.319, T.320 Chain C: D.260, V.278, A.279, G.297, Q.298, M.314, A.315, Q.316 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.264, B:A.266, B:A.284, C:A.279, C:A.315 Hydrogen bonds: B:Q.264 Water bridges: B:D.244, B:G.285 PLM.12: 20 residues within 4Å: Chain A: D.260, V.278, A.279, G.297, Q.298, M.314, A.315, Q.316 Chain C: F.210, Q.264, A.266, G.282, I.283, A.284, G.300, I.301, T.302, G.318, V.319, T.320 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Q.264, C:T.302, C:T.320, A:V.278, A:A.279, A:A.315, A:Q.316 Hydrogen bonds: C:Q.264 Water bridges: C:F.210, C:D.244, C:G.285

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

EDO.4: 2 residues within 4Å: Chain A: H.310 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.310

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

BME.5: 7 residues within 4Å: Chain A: R.188, C.208, H.222 Chain B: Y.180, H.182, I.198, Q.200 No protein-ligand interaction detected (PLIP)

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

UD1.8: 17 residues within 4Å: Chain A: F.210, G.211, Y.212, H.267, Q.268, G.285, S.286, G.303, H.304 Chain B: E.52, I.53, T.62, F.63, L.64, D.65, N.66, Y.69 22 PLIP interactions: 11 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:I.53, B:E.54, B:T.62, B:F.63, B:D.65, B:N.66, B:N.66, B:Y.69, B:Y.69, A:F.210, A:Y.212, A:Y.212, A:Q.268, A:S.286, A:S.286, A:H.304 pi-Stacking: B:F.63, B:Y.69 Water bridges: A:G.303 Salt bridges: A:H.267, A:H.304, A:H.304

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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