SMTL ID : 6kka.2 (1 other biounit)

Xylanase J mutant from Bacillus sp. 41M-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.213, E.215, N.232, D.322 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.213, A:E.215, A:N.232, A:D.322, A:D.322 CA.2: 4 residues within 4Å: Chain A: Y.237, D.313, W.317, D.318 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.237, A:D.313, A:W.317, A:D.318, H2O.2 CA.3: 3 residues within 4Å: Chain A: N.44, L.46, E.183 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 7 residues within 4Å: Chain A: R.269, D.271, N.278, T.281, T.311, A.312 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.269, A:T.311 Salt bridges: A:D.271, A:D.271

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 7 residues within 4Å: Chain A: N.44, Y.80, Y.95, R.128, Q.142, E.183, Y.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.80, A:Y.80 Water bridges: A:R.128 Salt bridges: A:R.128, A:R.128

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.16, R.48, Y.84, W.86, I.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.16, A:R.48, A:Y.84, A:Y.84 Water bridges: A:R.48 GOL.7: 2 residues within 4Å: Chain A: N.78, Y.185 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain A: S.24, G.25, Q.38, W.39, S.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:Q.38 GOL.9: 2 residues within 4Å: Chain A: T.311 Ligands: EPE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.273 GOL.10: 1 residues within 4Å: Chain A: N.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.266, A:T.316 Water bridges: A:N.264

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

MPD.11: 4 residues within 4Å: Chain A: G.23, S.24, S.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.41 MPD.12: 5 residues within 4Å: Chain A: G.12, Y.13, K.51, L.198, I.200 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.13, A:K.51, A:I.200 Hydrogen bonds: A:L.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takita, T. et al., Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis. Enzyme.Microb.Technol. (2019)

Release Date

2019-09-04

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endo-1,4-beta-xylanase

Related Entries With Identical Sequence