SMTL ID : 4j09.1

Crystal Structure of LpxA bound to RJPXD33

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x THR- ASN- LEU- TYR- MET- LEU: Putative metabolite transport protein YjhB(Non-covalent)

THR-ASN-LEU-TYR-MET-LEU.1: 25 residues within 4Å: Chain A: Q.73, D.74, H.122, A.124, H.125, T.140, A.142, G.143, A.158, V.159, H.160, G.176, V.177, H.191 Chain B: M.118, I.134, A.136, N.137, I.152, G.154, G.155, M.170, G.172, G.173, I.186 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:I.134, B:I.152, B:I.152, B:I.186, A:A.142, A:A.158 Hydrogen bonds: B:G.155, B:G.173, A:Q.73, A:H.122, A:H.125, A:G.143, A:H.160 Water bridges: A:Q.73, A:H.125, A:H.160 THR-ASN-LEU-TYR-MET-LEU.8: 25 residues within 4Å: Chain B: Q.73, D.74, H.122, A.124, H.125, T.140, A.142, G.143, A.158, V.159, H.160, G.176, V.177, H.191 Chain C: M.118, I.134, A.136, N.137, I.152, G.154, G.155, M.170, G.172, G.173, I.186 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.142, B:A.158, C:I.134, C:I.152, C:I.152, C:I.186 Hydrogen bonds: B:Q.73, B:H.122, B:H.125, B:G.143, B:H.160, C:G.155, C:G.173 Water bridges: B:Q.73, B:H.125, B:H.160 THR-ASN-LEU-TYR-MET-LEU.15: 25 residues within 4Å: Chain A: M.118, I.134, A.136, N.137, I.152, G.154, G.155, M.170, G.172, G.173, I.186 Chain C: Q.73, D.74, H.122, A.124, H.125, T.140, A.142, G.143, A.158, V.159, H.160, G.176, V.177, H.191 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:I.134, A:I.152, A:I.152, A:I.186, C:A.142, C:A.158 Hydrogen bonds: A:G.155, A:G.173, C:Q.73, C:G.143, C:H.160 Water bridges: C:Q.73, C:Q.73, C:H.125, C:H.160

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

PO4.2: 4 residues within 4Å: Chain A: R.216, K.220, R.224 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.216, A:K.220, A:R.224 PO4.3: 5 residues within 4Å: Chain A: G.41, V.43, D.59, N.60, E.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.59 PO4.4: 2 residues within 4Å: Chain A: R.100 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.77 Salt bridges: A:R.100 PO4.9: 4 residues within 4Å: Chain B: R.216, K.220, R.224 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.216, B:K.220, B:R.224 PO4.10: 5 residues within 4Å: Chain B: G.41, V.43, D.59, N.60, E.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.59 PO4.11: 2 residues within 4Å: Chain B: R.100 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.77, B:Y.77 Salt bridges: B:R.100 PO4.16: 4 residues within 4Å: Chain C: R.216, K.220, R.224 Ligands: EDO.20 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.216, C:K.220, C:R.224 PO4.17: 5 residues within 4Å: Chain C: G.41, V.43, D.59, N.60, E.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.59 PO4.18: 2 residues within 4Å: Chain C: R.100 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Y.77, C:Y.77 Salt bridges: C:R.100

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: R.91, D.114, N.115, L.116, R.132, C.133, I.134 Chain C: L.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.132 DMS.12: 8 residues within 4Å: Chain A: L.75 Chain B: R.91, D.114, N.115, L.116, R.132, C.133, I.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.132 DMS.19: 8 residues within 4Å: Chain B: L.75 Chain C: R.91, D.114, N.115, L.116, R.132, C.133, I.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.132

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

EDO.6: 7 residues within 4Å: Chain A: G.196, V.197, R.216, Y.219, K.220, R.224 Ligands: PO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.197, A:R.216, A:R.216, A:R.216 EDO.7: 6 residues within 4Å: Chain A: G.33, P.34, H.35, N.51, G.52 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.35, A:G.52 Water bridges: A:G.33 EDO.13: 7 residues within 4Å: Chain B: G.196, V.197, R.216, Y.219, K.220, R.224 Ligands: PO4.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.197, B:R.216, B:R.216, B:R.216 EDO.14: 6 residues within 4Å: Chain B: G.33, P.34, H.35, N.51, G.52 Ligands: PO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.52 Water bridges: B:G.33, B:H.35 EDO.20: 7 residues within 4Å: Chain C: G.196, V.197, R.216, Y.219, K.220, R.224 Ligands: PO4.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.197, C:R.216, C:R.216, C:R.216 EDO.21: 6 residues within 4Å: Chain C: G.33, P.34, H.35, N.51, G.52 Ligands: PO4.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.35, C:G.52 Water bridges: C:G.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenkins, R.J. et al., Structural Basis for the Recognition of Peptide RJPXD33 by Acyltransferases in Lipid A Biosynthesis. J.Biol.Chem. (2014)

Release Date

2014-04-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

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

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