SMTL ID : 2xvl.1

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with Pentaerythritol propoxylate (5 4 PO OH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

3 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain A: N.503, H.882, E.885 Ligands: CL.8, CL.9, CL.10, CL.11, CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.882 NI.2: 2 residues within 4Å: Chain A: H.500 Ligands: CL.14 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.500, H2O.2, H2O.5, H2O.5, H2O.13 NI.3: 1 residues within 4Å: Chain A: H.700 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.700, H2O.3, H2O.7, H2O.7, H2O.19

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

SO4.4: 2 residues within 4Å: Chain A: E.847, T.856 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.858 SO4.5: 3 residues within 4Å: Chain A: I.157, H.158, E.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.237 Water bridges: A:E.237 Salt bridges: A:H.158 SO4.6: 3 residues within 4Å: Chain A: D.164, K.401, E.611 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.164 Salt bridges: A:K.401

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

CL.7: 1 residues within 4Å: Chain A: K.461 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: N.503 Ligands: NI.1, CL.9, CL.11, CL.12 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: Q.881, E.885 Ligands: NI.1, CL.8, CL.10, CL.11 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: E.885 Ligands: NI.1, CL.9, CL.11, CL.12 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Ligands: NI.1, CL.8, CL.9, CL.10, CL.12 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: N.503, H.882 Ligands: NI.1, CL.8, CL.10, CL.11 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Ligands: NI.2 Ligand excluded by PLIP

1 x PXN: (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol(Non-covalent)

PXN.13: 7 residues within 4Å: Chain A: W.347, E.442, W.471, W.542, D.587, S.590, F.692 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.471, A:W.542, A:W.542 Hydrogen bonds: A:W.471, A:D.587 Water bridges: A:N.206, A:R.642, A:D.659

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsbrink, J. et al., Structural and Enzymatic Characterisation of a Glycoside Hydrolase Family 31 Alpha-Xylosidase from Cellvibrio Japonicus Involved in Xyloglucan Saccharification. Biochem.J. (2011)

Release Date

2011-04-13

Peptides

ALPHA-XYLOSIDASE, PUTATIVE, XYL31A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ALPHA-XYLOSIDASE, PUTATIVE, XYL31A

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