SMTL ID : 6haa.2 (1 other biounit)

Structure of a covalent complex of endo-Xyloglucanase from Cellvibrio japonicus after reacting with XXXG(2F)-beta-DNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x G2F- BGC- BGC- BGC- XYS- XYS- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose

G2F-BGC-BGC-BGC-XYS-XYS-XYS.1: 14 residues within 4Å: Chain A: N.60, A.70, W.71, G.72, H.136, W.137, N.182, Y.253, E.318, W.360, N.362, G.364, D.366, S.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.70, A:H.136 Halogen bonds: A:N.182, A:N.182 Water bridges: A:W.137, A:E.143, A:N.144

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.110, A.111, A.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.111, A:A.112

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

SO4.3: 2 residues within 4Å: Chain A: H.236, M.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.237, A:M.237

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

MES.4: 3 residues within 4Å: Chain A: N.188, A.189, E.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.189, A:E.190 Salt bridges: A:E.190

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 5 residues within 4Å: Chain A: L.25, Y.26, Q.104, E.105, E.153 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, N. et al., Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases. Org. Biomol. Chem. (2018)

Release Date

2018-10-03

Peptides

Cellulase, putative, cel5D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cellulase, putative, cel5D

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