SMTL ID : 6q7i.1

GH3 exo-beta-xylosidase (XlnD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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.1: 19 residues within 4Å: Chain A: N.122, T.124, L.125, Q.128, T.131, T.135, K.198, T.379, A.381, W.382, N.383, I.384, E.391, D.672, R.698, L.699, G.700 Ligands: EDO.16, EDO.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.381 Hydrogen bonds: A:Q.128, A:Q.128

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: N.680, T.681, T.682, S.734, E.736, R.743 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.743 NAG-NAG.4: 6 residues within 4Å: Chain B: N.680, T.681, T.682, S.734, E.736, R.743 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.743

1 x NAG- NAG- BMA- MAN- 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-(1-2)-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-MAN.3: 17 residues within 4Å: Chain B: N.122, T.124, L.125, Q.128, T.131, T.135, K.198, T.379, A.381, W.382, N.383, I.384, E.387, E.391, R.698, L.699, G.700 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.128 Water bridges: B:Q.128, B:Q.128

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

NAG.5: 3 residues within 4Å: Chain A: Q.23, H.24, N.26 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.593, T.595, S.596 Ligand excluded by PLIP NAG.7: 7 residues within 4Å: Chain A: N.3, T.4, S.5, Y.6, T.7, Y.9, N.298 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.658, T.711 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: D.63, E.64, N.67, L.74 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.104, W.373, D.374, L.377 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.419, R.443, Y.451 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: L.453, N.456, S.463 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: R.495, E.496, N.497 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain B: N.3, T.4, S.5, Y.6, T.7, Y.9, N.298 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Q.23, N.26 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.419, Y.451 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: L.453, N.456, S.463 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.593, T.595, S.596 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: D.63, N.67, L.74 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.658, T.711 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.104, T.372, W.373, D.374 Ligand excluded by PLIP

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 4 residues within 4Å: Chain A: R.219, Y.255, E.491 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.219, A:Y.255, A:Y.255 EDO.16: 6 residues within 4Å: Chain A: N.122, K.123, T.124, D.697, R.698 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.123, A:T.124 Water bridges: A:T.124, A:R.698 EDO.17: 6 residues within 4Å: Chain A: H.127, T.186, A.187, G.190, G.191 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186 Water bridges: A:T.186 EDO.18: 7 residues within 4Å: Chain A: T.131, S.134, A.187, G.190, K.198 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:A.187, A:K.198 EDO.32: 4 residues within 4Å: Chain B: P.237, I.240, V.241, R.728 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.728, B:R.728 Water bridges: B:R.244 EDO.33: 2 residues within 4Å: Chain B: P.687, Y.688 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.688, B:Y.688 Water bridges: B:K.690 EDO.34: 3 residues within 4Å: Chain B: R.495, E.496, N.497 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.496, B:N.497, B:N.497 Water bridges: B:D.494, B:D.494 EDO.35: 6 residues within 4Å: Chain B: E.233, W.605, P.689, W.692, A.720, R.721 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.720 EDO.36: 4 residues within 4Å: Chain B: L.17, W.87, Y.428, E.491 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.428, B:E.491 EDO.37: 3 residues within 4Å: Chain B: Y.182, D.245 Ligands: EDO.38 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.245 Water bridges: B:D.245, B:D.245 EDO.38: 3 residues within 4Å: Chain B: V.179, Y.182 Ligands: EDO.37 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 4 residues within 4Å: Chain A: F.18, P.19, L.20, W.328 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.18, A:P.19, A:L.20, A:W.328 Hydrogen bonds: A:L.20

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 12 residues within 4Å: Chain A: E.89, Y.151, R.165, K.204, H.205, R.219, M.252, Y.255, D.289, Y.428, E.491 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.89, A:R.165, A:R.165, A:K.204, A:R.219 GOL.20: 3 residues within 4Å: Chain A: V.179, Y.182, D.245 No protein-ligand interaction detected (PLIP) GOL.39: 10 residues within 4Å: Chain B: E.89, Y.151, R.165, K.204, H.205, R.219, Y.255, D.289, Y.428, E.491 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.89, B:R.165, B:R.165, B:H.205, B:R.219, B:E.491

4 x K: POTASSIUM ION(Non-covalent)

K.21: 2 residues within 4Å: Chain A: P.416, N.419 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.416, A:N.419, H2O.9, H2O.23, H2O.24, H2O.28 K.22: 2 residues within 4Å: Chain A: Y.579, Y.606 No protein-ligand interaction detected (PLIP) K.23: 3 residues within 4Å: Chain A: P.644, H.645, S.646 No protein-ligand interaction detected (PLIP) K.40: 2 residues within 4Å: Chain B: Y.579, Y.606 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, S.P. et al., Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes. Acs Cent.Sci. (2019)

Release Date

2019-06-05

Peptides

Exo-1,4-beta-xylosidase xlnD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Exo-1,4-beta-xylosidase xlnD

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