SMTL ID : 3c7o.1

Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with cellotetraose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC-BGC-BGC.1: 12 residues within 4Å: Chain A: F.56, W.101, G.124, W.160, F.162, F.224, E.225, F.244, G.286, G.287, N.288 Ligands: GOL.5 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.359, E.361, N.383, Q.384, D.480 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.359, A:E.361, A:Q.384, A:D.480, A:D.480

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

NA.3: 4 residues within 4Å: Chain A: R.368, S.388, Q.390, D.393 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.390, A:D.393 NA.4: 3 residues within 4Å: Chain A: P.103, P.164, H.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.290

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: D.24, F.56, L.59, W.101, F.162, D.163, E.225, R.321 Ligands: BGC-BGC-BGC-BGC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.163, A:R.321, A:R.321 Water bridges: A:H.290 GOL.6: 6 residues within 4Å: Chain A: P.146, L.147, S.151, T.152, P.153 Ligands: FMT.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.146 Water bridges: A:S.151

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 7 residues within 4Å: Chain A: A.415, S.416, T.417, A.445, N.475, L.476, F.477 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.416, A:T.417, A:T.417, A:N.475 Water bridges: A:G.419, A:N.475, A:N.478 FMT.8: 5 residues within 4Å: Chain A: T.217, I.218, D.219, P.268, F.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.219, A:F.269 FMT.9: 3 residues within 4Å: Chain A: P.153, V.211 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) FMT.10: 3 residues within 4Å: Chain A: N.326, K.327, G.345 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.326, A:K.327, A:K.327 Water bridges: A:K.327, A:N.342, A:N.342, A:G.345 FMT.11: 4 residues within 4Å: Chain A: A.27, L.28, T.29 Ligands: FMT.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.29 FMT.12: 2 residues within 4Å: Chain A: K.52, D.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.53, A:K.318, A:K.318 FMT.13: 3 residues within 4Å: Chain A: F.294, N.295 Ligands: FMT.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.295, A:N.295 FMT.14: 4 residues within 4Å: Chain A: N.31, G.32, F.296, K.297 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.32, A:K.297 Water bridges: A:N.298 FMT.15: 4 residues within 4Å: Chain A: N.353, P.354, Y.355, D.401 No protein-ligand interaction detected (PLIP) FMT.16: 2 residues within 4Å: Chain A: N.298, E.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.299 FMT.17: 3 residues within 4Å: Chain A: N.342, Y.343, A.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.343, A:A.344 Water bridges: A:N.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vandermarliere, E. et al., Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family. Biochem.J. (2009)

Release Date

2008-11-18

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase

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