SMTL ID : 4b3u.2 (1 other biounit)

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NWL: 6-amino-1-benzyl-5-(ethylamino)pyrimidine-2,4(1H,3H)-dione(Non-covalent)

NWL.1: 12 residues within 4Å: Chain A: L.55, Y.124, G.125, H.129, V.260, A.261, E.265, I.266, R.269, Q.270 Chain C: R.229 Ligands: GOL.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.55, A:Y.124, A:R.269, A:Q.270 Hydrogen bonds: A:A.261 Water bridges: A:K.259, A:C.262 pi-Cation interactions: C:R.229 NWL.6: 10 residues within 4Å: Chain B: L.55, H.129, V.260, A.261, E.265, I.266, R.269, Q.270 Chain D: R.229 Ligands: GOL.8 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:R.229, B:L.55, B:I.266, B:R.269 pi-Cation interactions: D:R.229 Hydrogen bonds: B:K.259, B:A.261 Water bridges: B:C.262 NWL.10: 12 residues within 4Å: Chain A: R.229 Chain C: L.55, Y.124, G.125, H.129, V.260, A.261, E.265, I.266, R.269, Q.270 Ligands: GOL.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.55, C:Y.124, C:R.269, C:Q.270 Hydrogen bonds: C:A.261 Water bridges: C:K.259, C:C.262 pi-Cation interactions: A:R.229 NWL.15: 10 residues within 4Å: Chain B: R.229 Chain D: L.55, H.129, V.260, A.261, E.265, I.266, R.269, Q.270 Ligands: GOL.17 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.55, D:I.266, D:R.269, B:R.229 Hydrogen bonds: D:K.259, D:A.261 Water bridges: D:C.262 pi-Cation interactions: B:R.229

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: H.126, D.127 Chain C: G.228, R.229, G.230 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.126, D.127 Chain D: G.228, R.229, G.230 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: G.228, R.229, G.230 Chain C: H.126, D.127 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: G.228, R.229, G.230 Chain D: H.126, D.127 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Y.48, S.51, T.52, L.55, Y.123, F.128, V.260, A.261 Ligands: NWL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.52, A:T.52, A:Y.123, A:A.261 GOL.4: 5 residues within 4Å: Chain A: H.239, L.242, L.243 Chain B: P.39, Y.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.243 GOL.8: 9 residues within 4Å: Chain B: Y.48, S.51, T.52, L.55, Y.123, F.128, V.260, A.261 Ligands: NWL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.52, B:Y.123, B:A.261 GOL.12: 9 residues within 4Å: Chain C: Y.48, S.51, T.52, L.55, Y.123, F.128, V.260, A.261 Ligands: NWL.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.52, C:Y.123, C:A.261 GOL.13: 5 residues within 4Å: Chain C: H.239, L.242, L.243 Chain D: P.39, Y.41 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.239, C:L.243 GOL.17: 9 residues within 4Å: Chain D: Y.48, S.51, T.52, L.55, Y.123, F.128, V.260, A.261 Ligands: NWL.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.52, D:Y.123, D:A.261

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 6 residues within 4Å: Chain A: F.160, G.164, A.166, V.224, I.226 Chain C: Y.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.166, A:V.224 Water bridges: A:I.226 MES.9: 9 residues within 4Å: Chain B: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 Chain D: Y.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.166, B:V.224 Water bridges: B:I.226 MES.14: 6 residues within 4Å: Chain A: Y.303 Chain C: F.160, G.164, A.166, V.224, I.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.166, C:V.224 Water bridges: C:I.226 MES.18: 9 residues within 4Å: Chain B: Y.303 Chain D: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.166, D:V.224 Water bridges: D:I.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alphey, M.S. et al., Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa. ACS Chem. Biol. (2013)

Release Date

2012-10-31

Peptides

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE

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