SMTL ID : 4xx6.1 (1 other biounit)

Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: P.24, H.25, N.28, H.31, D.32, L.246, D.284, L.285, Y.286, P.290, P.294, G.295, D.304 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 6 residues within 4Å: Chain A: L.27, H.31, E.51, N.65, I.71 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.27, A:I.71

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain A: N.138, N.140, T.142, R.144, E.145 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.145, A:T.150, A:N.138, A:E.145

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 6 residues within 4Å: Chain A: L.21, G.22, V.23, E.49, N.50, E.51 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.140, N.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: D.80 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, H2O.3, H2O.7

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

PEG.7: 6 residues within 4Å: Chain A: Y.91, R.144, E.145, N.146, V.147 Ligands: NAG-NAG-BMA-MAN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.144, A:V.147

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 10 residues within 4Å: Chain A: R.9, A.10, P.14, R.15, Y.16, N.44, D.80, V.82, Y.128, V.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.9, A:N.44 P6G.9: 6 residues within 4Å: Chain A: L.26, L.27, F.29, D.36, A.74, A.78 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: E.254, A.257, R.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.254 GOL.11: 3 residues within 4Å: Chain A: Y.149, G.153, P.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.149 GOL.12: 5 residues within 4Å: Chain A: E.135, Y.178, Q.209, H.211, W.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.135 Water bridges: A:Y.178, A:Y.293 GOL.13: 1 residues within 4Å: Chain A: A.162 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum. To Be Published

Release Date

2015-02-11

Peptides

Beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-xylanase

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