SMTL ID : 6jdz.1 (1 other biounit)

Ligand complex structure of GH10 family xylanase XynAF1, soaking for 20 minutes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

2 x XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose(Non-covalent)

XYP-XYP.1: 13 residues within 4Å: Chain A: N.46, K.49, H.82, W.86, Q.89, N.130, E.131, Q.206, E.238, W.278, W.286 Ligands: XYP-XYP.2, GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.46, A:K.49, A:W.278 Water bridges: A:N.46 XYP-XYP.2: 10 residues within 4Å: Chain A: W.86, E.131, Y.174, N.175, Q.206, H.208, R.242, W.286, F.291 Ligands: XYP-XYP.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.86, A:E.131

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 6 residues within 4Å: Chain A: N.101, L.105, I.147, I.148, A.151 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.101, A:I.148 Water bridges: A:I.148

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.4, K.8, K.13, G.40, G.76, L.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.4, A:N.4 GOL.5: 5 residues within 4Å: Chain A: S.179, G.180, A.183, T.184, Q.187 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.180, A:G.180, A:T.184, A:Q.187 Water bridges: A:S.179, A:S.179, A:V.223 GOL.6: 10 residues within 4Å: Chain A: D.20, E.23, G.45, N.46, W.278, D.279, Y.284, S.285, W.286 Ligands: XYP-XYP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.45, A:D.279, A:Y.284 Water bridges: A:W.286

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

MES.7: 4 residues within 4Å: Chain A: Y.178, S.213, T.214, P.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.179, A:S.179

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: K.109, I.155, T.159 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G. et al., Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5. To Be Published

Release Date

2020-05-20

Peptides

Beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-xylanase

Related Entries With Identical Sequence