SMTL ID : 5a6m.1

Determining the specificities of the catalytic site from the very high resolution structure of the thermostable glucuronoxylan endo-Beta-1, 4-xylanase, CtXyn30A, from Clostridium thermocellum with a xylotetraose bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

1 x XYS- XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose

XYS-XYP-XYP.1: 11 residues within 4Å: Chain A: W.46, W.104, N.158, E.159, E.165, W.166, Y.223, A.248, W.287 Ligands: XYP-XYP.2, PO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.165, A:E.165, A:W.104, A:N.158, A:E.159, A:E.159

1 x XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose(Non-covalent)

XYP-XYP.2: 9 residues within 4Å: Chain A: E.159, Y.162, W.166, F.195, Q.196, Y.223, G.224, Y.250 Ligands: XYS-XYP-XYP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.250, A:Y.250

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: R.176, R.179 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.176, A:R.176 Salt bridges: A:R.176, A:R.179 PO4.4: 1 residues within 4Å: Chain A: K.123 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.123 PO4.5: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.257 PO4.6: 6 residues within 4Å: Chain A: W.287, Y.288, R.291, Y.293 Ligands: XYS-XYP-XYP.1, XYS-XYP-XYP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.287, A:Y.293 Water bridges: A:Y.288, A:R.291, A:R.291, A:R.291, A:R.291 Salt bridges: A:R.291 PO4.7: 4 residues within 4Å: Chain A: Y.250, N.253, S.254, D.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.250, A:S.254, A:S.254

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: V.141, D.150, L.151, Y.152, N.186, C.187, R.188 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.186 Water bridges: A:L.151, A:Y.152, A:R.188, A:R.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freire, F. et al., Conservation in the Mechanism of Glucuronoxylan Hydrolysis Revealed by the Structure of Glucuronoxylan Xylano-Hydrolase (Ctxyn30A) from Clostridium Thermocellum. Acta Crystallogr.,Sect.D (2016)

Release Date

2016-10-19

Peptides

CARBOHYDRATE BINDING FAMILY 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CARBOHYDRATE BINDING FAMILY 6

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