SMTL ID : 5gqd.1

Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x XYS- XYP: beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose(Post Translational Modification)

XYS-XYP.1: 12 residues within 4Å: Chain A: E.44, N.45, K.48, H.81, W.85, Q.88, H.128, N.170, Q.205, E.236, W.266, W.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.44, A:N.45, A:W.266, A:K.48, A:H.81, A:H.128, A:N.170, A:Q.205 Water bridges: A:N.45, A:Q.88, A:W.274 XYS-XYP.2: 13 residues within 4Å: Chain B: E.44, N.45, K.48, H.81, W.85, Q.88, H.128, N.170, Q.205, E.236, W.266, W.274 Ligands: GOL.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.44, B:E.44, B:N.45, B:K.48, B:W.266, B:K.48, B:H.81, B:S.127, B:S.127, B:N.170, B:Q.205 Water bridges: B:W.274

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: T.4, G.6, A.7, S.35, R.36, E.37, F.38, N.39, N.74, G.75, K.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.6, A:A.7, A:R.36, A:N.74 GOL.4: 8 residues within 4Å: Chain A: D.408, A.409, V.410, G.411, G.412, Q.421, Y.423, N.430 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.409, A:G.411, A:G.412, A:Q.421, A:N.430, A:Q.431 Water bridges: A:Q.421, A:S.426, A:N.430 GOL.5: 8 residues within 4Å: Chain A: D.325, V.326, P.327, N.328, Q.338, Y.340, H.343, N.347 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.326, A:N.328, A:Q.338, A:H.343, A:N.347 Water bridges: A:N.328, A:N.328, A:Q.338 GOL.6: 8 residues within 4Å: Chain A: A.368, A.369, G.370, N.387, Q.402 Chain B: S.210, G.211, Q.240 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.210, B:S.210, B:Q.240, A:N.387, A:Q.402, A:Q.402 Water bridges: B:S.210, B:D.278 GOL.7: 10 residues within 4Å: Chain A: A.355, E.357, R.359, W.383, G.384 Chain B: A.355, E.357, W.383, G.384, K.389 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.383, B:K.389, B:K.389, A:E.357, A:R.359 Water bridges: B:R.359, B:R.359, A:G.385 GOL.8: 8 residues within 4Å: Chain B: D.325, V.326, P.327, N.328, Q.338, Y.340, H.343, N.347 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.328, B:Q.338, B:H.343, B:N.347 Water bridges: B:N.328, B:Q.338 GOL.9: 8 residues within 4Å: Chain B: D.408, A.409, V.410, G.411, G.412, Q.421, Y.423, N.430 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.409, B:G.411, B:G.412, B:Q.421, B:N.430 Water bridges: B:S.426 GOL.10: 5 residues within 4Å: Chain B: H.128, Y.172, Q.205, W.274 Ligands: XYS-XYP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, R. et al., Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant. J.Appl.Glyosci. (2019)

Release Date

2017-08-09

Peptides

Beta-xylanase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-xylanase

Related Entries With Identical Sequence