SMTL ID : 1od8.1

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: T.294, L.297, D.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.298 Water bridges: A:L.297 NA.2: 3 residues within 4Å: Chain A: D.298, G.302, G.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.298, A:G.303 Water bridges: A:D.298 NA.3: 2 residues within 4Å: Chain A: E.2, S.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.2, A:S.3, A:S.3 Water bridges: A:T.4 NA.10: 1 residues within 4Å: Chain A: T.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.3

2 x XDL: XYLOSE-DERIVED ISOFAGOMINE LACTAM(Non-covalent)

XDL.4: 6 residues within 4Å: Chain A: D.132, N.173, W.179, G.211, S.212 Ligands: XYP.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.132, A:G.133 XDL.8: 11 residues within 4Å: Chain A: K.48, H.81, W.85, N.127, E.128, Q.205, E.236, W.266, W.274 Ligands: IMD.7, XYP.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.274 Hydrogen bonds: A:K.48, A:H.81, A:N.127, A:E.128, A:Q.205

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

XYP.5: 8 residues within 4Å: Chain A: D.132, Y.172, N.173, N.209, S.212, R.275 Ligands: XDL.4, IMD.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.173, A:N.209, A:S.212, A:R.275, A:R.275 Water bridges: A:D.132, A:S.212, A:S.212 XYP.9: 7 residues within 4Å: Chain A: E.44, N.45, K.48, Q.88, W.266, W.274 Ligands: XDL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.44, A:N.45, A:W.266 Water bridges: A:W.274 Salt bridges: A:K.48

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 5 residues within 4Å: Chain A: G.13, R.14, S.258, C.260, L.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.258 Water bridges: A:Y.15 IMD.7: 8 residues within 4Å: Chain A: E.128, Y.172, Q.205, H.207, W.274, R.275 Ligands: XYP.5, XDL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.275 pi-Stacking: A:Y.172, A:W.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gloster, T.M. et al., A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds as its Amide Tautomer. Chem.Commun.(Camb.) (2003)

Release Date

2003-04-08

Peptides

ENDO-1,4-BETA-XYLANASE A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDO-1,4-BETA-XYLANASE A

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