SMTL ID : 7cpl.1

Xylanase R from Bacillus sp. TAR-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: D.287, Q.291, R.349, H.358, H.360 Ligands: MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.291 Hydrogen bonds: A:H.358, A:H.360 MPD.2: 4 residues within 4Å: Chain A: D.71, E.75, R.78, R.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.78, A:R.78 MPD.3: 6 residues within 4Å: Chain A: E.151, Q.226, H.228, E.257, W.309, W.317 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.309, A:W.317 Hydrogen bonds: A:E.257 Water bridges: A:E.151 MPD.4: 5 residues within 4Å: Chain A: R.349, E.354, H.356, H.358 Ligands: MPD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.349 MPD.5: 4 residues within 4Å: Chain A: S.14, E.15, Q.18, N.45 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.45 Hydrogen bonds: A:N.45 MPD.6: 2 residues within 4Å: Chain A: K.211, L.249 No protein-ligand interaction detected (PLIP) MPD.7: 3 residues within 4Å: Chain A: Y.274, N.314, H.339 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.274, A:H.339 Water bridges: A:N.314

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: D.290, R.349, D.352 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:R.349, H2O.2, H2O.2, H2O.4, H2O.5 CA.9: 3 residues within 4Å: Chain A: Q.20, A.300, I.303 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.20, A:A.300, A:I.303, H2O.10, H2O.10 CA.10: 5 residues within 4Å: Chain A: Y.274, D.313, T.316, D.319, D.332 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.274, A:D.313, A:D.319, A:D.319, A:D.332 CA.11: 1 residues within 4Å: Chain A: D.276 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.276, A:D.276, H2O.11, H2O.11

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

NI.12: 4 residues within 4Å: Chain A: D.290, E.294, E.354, H.358 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.290, A:E.294, A:E.294, A:E.354, A:H.358 NI.13: 2 residues within 4Å: Chain A: D.22, E.83 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.22, A:D.22, A:E.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, M. et al., Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E. Biosci.Biotechnol.Biochem. (2021)

Release Date

2020-09-02

Peptides

Endo-1,4-beta-xylanase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase A