SMTL ID : 5fuh.2 (1 other biounit)

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x HKX: N-[6-amino-1-(3-bromobenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl]-N-methylbenzenesulfonamide(Non-covalent)

HKX.1: 17 residues within 4Å: Chain A: Y.48, S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Chain C: R.229 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.55, A:L.55, A:F.128, A:F.128, A:H.129, A:A.261 Hydrogen bonds: A:G.125, A:A.261 Water bridges: A:D.127, A:H.129, A:C.262, A:E.265 Halogen bonds: A:I.266 pi-Cation interactions: C:R.229 HKX.5: 16 residues within 4Å: Chain B: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 Chain D: R.229 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.55, B:F.128, B:F.128, B:H.129, B:A.261 Hydrogen bonds: B:A.261 Water bridges: B:F.128, B:C.262, B:E.265 pi-Cation interactions: D:R.229 HKX.10: 17 residues within 4Å: Chain A: R.229 Chain C: Y.48, S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.55, C:L.55, C:F.128, C:F.128, C:H.129, C:A.261 Hydrogen bonds: C:G.125, C:A.261 Water bridges: C:D.127, C:H.129, C:C.262, C:E.265 Halogen bonds: C:I.266 pi-Cation interactions: A:R.229 HKX.14: 16 residues within 4Å: Chain B: R.229 Chain D: S.51, T.52, L.55, Y.123, Y.124, G.125, F.128, H.129, K.259, V.260, A.261, E.265, I.266, R.269, Q.270 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.55, D:F.128, D:F.128, D:H.129, D:A.261 Hydrogen bonds: D:A.261 Water bridges: D:F.128, D:C.262, D:E.265 pi-Cation interactions: B:R.229

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

MES.2: 9 residues within 4Å: Chain A: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 Chain C: Y.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.166, A:V.224 MES.6: 8 residues within 4Å: Chain B: 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, B:V.224 MES.11: 9 residues within 4Å: Chain A: Y.303 Chain C: F.160, G.164, K.165, A.166, L.222, S.223, V.224, I.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.166, C:V.224 MES.15: 8 residues within 4Å: Chain B: Y.303 Chain D: 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, D:V.224

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

CL.3: 4 residues within 4Å: Chain A: H.126 Chain C: G.228, R.229, G.230 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: H.126 Chain D: G.228, R.229, G.230 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: G.228, R.229, G.230 Chain C: H.126 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: G.228, R.229, G.230 Chain D: H.126 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.253, G.257, K.259, Y.293, R.296 Chain C: L.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.253, A:K.259, A:R.296 Water bridges: A:Y.41, A:G.289 GOL.8: 5 residues within 4Å: Chain B: L.76, L.77, G.80, N.82, W.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.76, B:G.80, B:N.82 Water bridges: B:W.83 GOL.9: 7 residues within 4Å: Chain B: E.253, G.257, K.259, G.289, Y.293, R.296 Chain D: L.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.253, B:E.253, B:K.259, B:K.259, B:R.296 GOL.13: 6 residues within 4Å: Chain A: L.150 Chain C: E.253, G.257, K.259, Y.293, R.296 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.253, C:K.259, C:R.296 Water bridges: C:G.289 GOL.17: 5 residues within 4Å: Chain D: L.76, L.77, G.80, N.82, W.83 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.76, D:G.80, D:N.82 Water bridges: D:W.83, D:E.264 GOL.18: 7 residues within 4Å: Chain B: L.150 Chain D: E.253, G.257, K.259, G.289, Y.293, R.296 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.253, D:K.259, D:K.259, D:R.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, F. et al., Allosteric Competitive Inhibitors of the Glucose-1-Phosphate Thymidylyltransferase (Rmla) from Pseudomonas Aeruginosa. To be Published

Release Date

2017-02-22

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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