SMTL ID : 1r87.1

Crystal structure of the extracellular xylanase from Geobacillus stearothermophilus T-6 (XT6, monoclinic form): The complex of the WT enzyme with xylopentaose at 1.67A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

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

XYP-XYP.1: 11 residues within 4Å: Chain A: W.99, E.159, Y.203, N.204, Q.234, Q.238, W.241, W.273, W.324, R.328 Ligands: XYP-XYP-XYP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.328

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

XYP-XYP-XYP.2: 16 residues within 4Å: Chain A: E.58, N.59, K.62, H.95, W.99, Q.102, N.158, E.159, Q.234, H.236, E.265, W.316, W.324 Ligands: XYP-XYP.1, ZN.7, CL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:Q.102

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.11, D.365 Ligands: CL.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.11, A:D.365 ZN.4: 1 residues within 4Å: Chain A: D.21 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.21, H2O.6, H2O.6, H2O.6, H2O.6, H2O.6 ZN.5: 2 residues within 4Å: Chain A: D.282 Ligands: ZN.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.282, A:D.282, H2O.9 ZN.6: 2 residues within 4Å: Chain A: D.282 Ligands: ZN.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.282, H2O.7 ZN.7: 5 residues within 4Å: Chain A: E.35, E.58, H.322 Ligands: XYP-XYP-XYP.2, CL.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.58, A:E.58, A:H.322, H2O.1 ZN.8: 4 residues within 4Å: Chain A: E.27, S.307, I.310 Ligands: SO4.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:S.307, A:I.310, H2O.7, H2O.9 ZN.9: 4 residues within 4Å: Chain A: D.297, A.374, D.377, K.379 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.297, A:A.374, A:D.377, H2O.1, H2O.1

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

CL.10: 4 residues within 4Å: Chain A: H.11, Y.281, D.365 Ligands: ZN.3 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: E.58, H.322, W.324 Ligands: XYP-XYP-XYP.2, ZN.7 Ligand excluded by PLIP

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

SO4.12: 4 residues within 4Å: Chain A: N.26, E.27, S.307 Ligands: ZN.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.26, A:S.307, A:D.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zolotnitsky, G. et al., Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-07-20

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase

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