SMTL ID : 3u0x.1

Crystal structure of the B-specific-1,3-galactosyltransferase (GTB) in complex with compound 382

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GTI: 1-(3-phenyl-1,2,4-thiadiazol-5-yl)piperazine(Non-covalent)

GTI.1: 12 residues within 4Å: Chain A: D.155, D.157, M.158, P.178, S.179, M.210, A.212, W.269, D.270, L.273, L.274 Ligands: GOL.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.178, A:L.273, A:L.274 Hydrogen bonds: A:D.155, A:D.157 Water bridges: A:D.270, A:D.270 pi-Stacking: A:H.177 GTI.12: 11 residues within 4Å: Chain B: D.155, D.157, M.158, P.178, S.179, M.210, D.270, L.273, L.274, A.287 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.178, B:L.273, B:L.274 Hydrogen bonds: B:D.157 pi-Stacking: B:H.177

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

CL.2: 3 residues within 4Å: Chain A: F.188, R.192, K.202 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: P.11, R.12 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: GTI.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.189, A:E.247 Water bridges: A:S.179 GOL.5: 7 residues within 4Å: Chain A: Q.197, A.198, A.227, A.231, H.249, K.252, Y.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.197, A:H.249 Water bridges: A:A.227, A:A.231 GOL.6: 4 residues within 4Å: Chain A: D.270, Q.272, L.273, P.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.290 Water bridges: A:D.270, A:A.287 GOL.7: 3 residues within 4Å: Chain A: N.238, G.239 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.238 GOL.13: 8 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, M.210, W.244, E.247 Ligands: GTI.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.189, B:T.189, B:E.247 GOL.14: 7 residues within 4Å: Chain B: Q.197, A.198, A.227, A.231, H.249, K.252, Y.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.249 Water bridges: B:H.257

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

SO4.8: 2 residues within 4Å: Chain A: P.277, A.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.278 Water bridges: A:V.279 SO4.9: 3 residues within 4Å: Chain A: Q.113, S.115, R.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.113, A:S.115 Water bridges: A:V.116, A:R.143 Salt bridges: A:R.143 SO4.10: 4 residues within 4Å: Chain A: K.83, H.84, V.87, H.163 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.83, A:V.87, A:H.163, A:H.163 Salt bridges: A:H.84, A:H.163 SO4.11: 5 residues within 4Å: Chain A: R.193, G.239, I.240, E.241 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.239, A:E.241, A:E.241 Salt bridges: A:R.193 SO4.15: 2 residues within 4Å: Chain B: S.115, R.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.115 Water bridges: B:V.116 Salt bridges: B:R.143 SO4.16: 4 residues within 4Å: Chain B: K.83, H.84, V.87, H.163 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.83, B:H.84 Water bridges: B:V.87, B:H.163 Salt bridges: B:H.163 SO4.17: 9 residues within 4Å: Chain B: F.65, R.132, I.136, C.153, V.154, D.155, G.211, F.214, D.246 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.155 Water bridges: B:R.132, B:V.154, B:V.154 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jorgensen, R. et al., A novel compound from a molecular fragment library screen inhibits glycosyltransferases by displacing the metal ion and interfering with substrate binding. To be Published

Release Date

2012-10-24

Peptides

Histo-blood group ABO system transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histo-blood group ABO system transferase