SMTL ID : 6kjl.1

Xylanase J from Bacillus sp. strain 41M-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.214, E.216, N.233, D.323 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.214, A:E.216, A:N.233, A:D.323, H2O.5 CA.2: 5 residues within 4Å: Chain A: Y.238, D.314, W.318, D.319 Ligands: MPD.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:Y.238, A:D.314, A:W.318, A:D.319 CA.12: 4 residues within 4Å: Chain B: Y.238, D.314, W.318, D.319 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.238, B:D.314, B:W.318, B:D.319 CA.13: 4 residues within 4Å: Chain B: E.214, E.216, N.233, D.323 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.214, B:E.216, B:N.233, B:D.323, H2O.10

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

EPE.3: 6 residues within 4Å: Chain A: R.270, D.272, N.279, T.282, T.312, A.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.279 Salt bridges: A:D.272, A:D.272 EPE.4: 3 residues within 4Å: Chain A: Y.224, Y.238, A.239 No protein-ligand interaction detected (PLIP) EPE.14: 6 residues within 4Å: Chain B: R.270, D.272, N.279, T.282, T.312, A.313 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.279, B:T.312 Water bridges: B:N.279 Salt bridges: B:D.272, B:D.272

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

MPD.5: 10 residues within 4Å: Chain A: E.17, W.19, R.49, Y.85, W.87, S.134, I.135 Chain B: M.268, Y.284 Ligands: GOL.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.19, A:I.135, B:Y.284 Water bridges: A:E.17, A:E.17, A:R.49 MPD.6: 7 residues within 4Å: Chain A: N.264, N.265, G.316, T.317, W.318, D.319 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Water bridges: A:N.265 MPD.15: 4 residues within 4Å: Chain B: N.79, W.104, Y.186 Ligands: GOL.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.186 MPD.16: 10 residues within 4Å: Chain A: M.268, Y.284, Y.293 Chain B: E.17, W.19, R.49, Y.85, W.87, S.134, I.135 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.284, B:W.87, B:I.135 Hydrogen bonds: A:Y.293, B:E.17, B:R.49, B:R.49 MPD.17: 7 residues within 4Å: Chain A: D.12, G.13 Chain B: G.13, Y.14, G.51, K.52, L.199 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.52 Hydrogen bonds: B:Y.14, B:L.199, A:G.13 MPD.18: 6 residues within 4Å: Chain A: N.131, Q.132, P.133 Chain B: S.266, G.286, D.287 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.133 Hydrogen bonds: B:G.286

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: W.19, N.45, L.47, E.94, Y.96, R.129, E.184 Ligands: MPD.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.19, A:N.45, A:Y.96, A:R.129, A:E.184 Water bridges: A:R.129, A:Q.143 GOL.8: 6 residues within 4Å: Chain A: G.13, Y.14, K.52, L.199 Chain B: D.12, G.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:G.13, A:L.199, A:I.201 Hydrogen bonds: A:Y.14 GOL.9: 3 residues within 4Å: Chain A: N.265, S.266, N.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.266, A:S.266, A:N.267 Water bridges: A:N.265 GOL.10: 7 residues within 4Å: Chain A: G.64, N.65, G.202, Q.204, K.252, A.253, N.254 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.65, A:G.202, A:Q.204, A:K.252, A:A.253, A:N.254, A:N.254 Water bridges: A:S.160, A:S.160 GOL.11: 7 residues within 4Å: Chain A: S.27, M.28, T.29, S.37, A.38, Q.39, S.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.27, A:S.37, A:A.38, A:A.38 GOL.19: 6 residues within 4Å: Chain B: Y.81, Y.96, Q.143, W.145, E.184 Ligands: MPD.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.81, B:Q.143 GOL.20: 4 residues within 4Å: Chain B: A.2, I.3, T.4, S.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.2, B:T.4, B:S.5, B:S.5, B:E.7 GOL.21: 6 residues within 4Å: Chain B: W.101, G.102, T.103, W.104, R.105 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.102, B:R.105 GOL.22: 1 residues within 4Å: Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.105 GOL.23: 2 residues within 4Å: Chain B: Y.224, Y.238 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endo-1,4-beta-xylanase