SMTL ID : 5c0p.1

The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: T.158 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:T.158, H2O.1, H2O.6, H2O.8, H2O.9, H2O.9 MG.2: 2 residues within 4Å: Chain A: D.84, H.261 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.84, A:H.261, H2O.2, H2O.3, H2O.4, H2O.9

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

CL.3: 5 residues within 4Å: Chain A: F.68, A.70, K.71, F.74, P.121 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: L.32, Y.86, E.87 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.142, E.144, W.148, G.241, N.242, V.243 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.242, A:V.243 Water bridges: A:K.143, A:R.167, A:G.241 GOL.6: 4 residues within 4Å: Chain A: A.169, D.171, K.173, T.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.174, A:T.174 Water bridges: A:T.174 GOL.7: 3 residues within 4Å: Chain A: L.24, R.25, Y.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:N.46, A:Y.53 Water bridges: A:R.25 GOL.8: 4 residues within 4Å: Chain A: N.255, Y.276, T.289, I.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.276

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 9 residues within 4Å: Chain A: R.27, D.28, W.81, A.82, L.135, D.136, D.205, Y.231, H.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.27, A:D.205, A:Y.231, A:H.261 Water bridges: A:D.205, A:D.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482. To Be Published

Release Date

2015-07-01

Peptides

Endo-arabinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-arabinase