SMTL ID : 3t7d.1

Vall from streptomyces hygroscopicus in complex with trehalose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 14 residues within 4Å: Chain A: R.12, V.38, W.105, H.182, I.183, F.215, R.290, N.325, R.326, D.383, G.384, Q.385, N.386, L.387 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.160, A:R.290, A:N.325, A:R.326 Water bridges: A:R.12, A:R.12, A:R.12, A:K.295, A:R.326 Salt bridges: A:R.12 GLC-GLC.2: 14 residues within 4Å: Chain B: R.12, W.105, H.182, I.183, F.215, R.290, N.325, R.326, D.383, G.384, Q.385, N.386, L.387 Ligands: MG.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.12, B:Q.160, B:R.290, B:N.325 Water bridges: B:D.292

18 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.11, T.100, Q.160, R.326 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: R.78, S.260, P.261, L.262, E.461 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.260, A:E.461 MG.5: 3 residues within 4Å: Chain A: R.249, D.474, A.477 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.474, H2O.5 MG.6: 5 residues within 4Å: Chain A: L.231, P.232, D.233, W.245, R.246 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: G.266, R.267 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: R.125, K.196, E.197 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: S.119 Chain B: R.299, R.302 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.119 MG.10: 4 residues within 4Å: Chain A: A.13, I.15, D.55, D.59 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.55, A:D.59, A:D.59 MG.11: 5 residues within 4Å: Chain A: M.104, Y.159, V.162, I.202 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain A: M.104, A.107, N.108 Ligands: MG.11 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain B: K.11, R.12, T.100, Y.159, Q.160, R.326 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.100 MG.16: 5 residues within 4Å: Chain B: L.207, V.243, W.245, H.248, T.250 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.250 MG.17: 6 residues within 4Å: Chain B: A.188, W.191, R.192, S.226, D.229, L.230 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.188 MG.18: 3 residues within 4Å: Chain B: G.289, R.290, K.295 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain A: K.196 Chain B: E.406, S.420, V.421 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.406, B:S.420 MG.20: 5 residues within 4Å: Chain B: W.105, D.292, R.326 Ligands: GLC-GLC.2, MG.21 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.292, H2O.18, H2O.19 MG.21: 6 residues within 4Å: Chain B: W.105, D.292, P.293, N.332 Ligands: MG.20, MG.22 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain B: A.101, W.105, V.329, N.332 Ligands: MG.21 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.101, H2O.18, H2O.19

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.13: 4 residues within 4Å: Chain B: V.153, P.176, L.468, A.472 No protein-ligand interaction detected (PLIP) IMD.14: 2 residues within 4Å: Chain B: N.47, E.79 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structural basis for the substrate specificity of ValL. To be Published

Release Date

2012-08-01

Peptides

Putative glycosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative glycosyltransferase