SMTL ID : 6qe8.1

Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 9 residues within 4Å: Chain A: D.64, Y.93, Y.108, Q.156, F.158, E.197, W.199 Ligands: SO4.7, HZB.10 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.64, A:Q.156 Salt bridges: A:E.197 pi-Cation interactions: A:W.199

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

SO4.2: 3 residues within 4Å: Chain A: S.86, A.87, S.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.88, A:S.88, A:S.88 Water bridges: A:A.87, A:A.87, A:G.89 SO4.3: 3 residues within 4Å: Chain A: N.144, S.152, T.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.153, A:T.153 Water bridges: A:S.152 SO4.4: 2 residues within 4Å: Chain A: T.171, N.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.174 SO4.5: 1 residues within 4Å: Chain A: T.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166 Water bridges: A:Y.85, A:D.112, A:T.166 SO4.6: 4 residues within 4Å: Chain A: N.36, G.39, N.40, F.44 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.36, A:N.36 Water bridges: A:F.44, A:F.44 SO4.7: 6 residues within 4Å: Chain A: R.142, E.145, F.154, Q.156 Ligands: MES.1, HZB.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.145 Water bridges: A:Q.156 Salt bridges: A:R.142 SO4.8: 3 residues within 4Å: Chain A: A.122, T.123, S.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.124, A:S.124 SO4.9: 1 residues within 4Å: Chain A: R.142 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.142

1 x HZB: (1~{R},3~{S},4~{R},5~{R})-5-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexane-1,2,3,4-tetrol(Covalent)

HZB.10: 16 residues within 4Å: Chain A: Q.35, D.64, V.66, Y.97, W.99, E.106, Y.108, P.146, S.147, I.148, F.154, Q.156, Y.191, E.197 Ligands: MES.1, SO4.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.106 Hydrogen bonds: A:Q.35, A:Q.35, A:Y.97, A:Y.97, A:Y.108, A:Y.108, A:P.146, A:S.147, A:Q.156, A:Y.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, S.P. et al., Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes. Acs Cent.Sci. (2019)

Release Date

2019-06-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase A