SMTL ID : 6q7j.1

GH3 exo-beta-xylosidase (XlnD) in complex with xylobiose aziridine activity based probe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

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.1: 15 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.387, E.391, R.698 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.128, A:Q.128

1 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 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-(1-6)-[alpha-D-mannopyranose-(1-3)]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.3: 15 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, E.387, E.391, D.672, R.698 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.128, B:Q.128

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

NAG.4: 2 residues within 4Å: Chain A: Q.23, N.26 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.593, T.595, S.596 Ligand excluded by PLIP NAG.6: 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.7: 2 residues within 4Å: Chain A: N.658, T.711 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: D.63, E.64, N.67, L.74 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.104, W.373, D.374 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.419, R.443, Y.451 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.456, G.464 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.215, N.216, E.496 Ligand excluded by PLIP NAG.16: 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.17: 2 residues within 4Å: Chain B: N.593, S.596 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: Q.23, H.24, N.26 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.658 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: D.63, N.67, L.74 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: N.680, T.681, S.734, Y.735, R.743 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.104, W.373, D.374, L.377 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: L.453, N.456 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.419, Y.451 Ligand excluded by PLIP

2 x HLB: 5-[3,3-dimethyl-2-[5-(1,3,3-trimethylindol-2-ylidene)penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[8-[[(1~{R},2~{S},3~{S},4~{S},5~{R})-2,3,4,5-tetrakis(oxidanyl)cyclohexyl]amino]octyl]pentanamide(Covalent)

HLB.13: 15 residues within 4Å: Chain A: N.14, P.15, W.87, E.89, Y.151, R.165, K.204, H.205, R.219, M.252, Y.255, D.289, C.290, Y.428, E.491 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.87, A:Y.255, A:D.289 Hydrogen bonds: A:R.165, A:R.165, A:K.204, A:H.205, A:R.219, A:Y.255, A:E.491, A:E.491 HLB.25: 14 residues within 4Å: Chain B: N.14, E.89, Y.151, R.165, K.204, H.205, Y.209, R.219, M.252, Y.255, D.289, C.290, Y.428, E.491 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.255, B:D.289 Hydrogen bonds: B:R.165, B:R.165, B:K.204, B:H.205, B:R.219, B:Y.428, B:E.491, B:E.491

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

EDO.14: 5 residues within 4Å: Chain A: P.644, H.645, S.646, Y.648, K.654 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.646, A:S.646 Water bridges: A:P.644 EDO.15: 3 residues within 4Å: Chain A: L.22, R.96, Y.428 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain B: F.18, P.19, L.20, W.328 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.20 EDO.27: 6 residues within 4Å: Chain A: S.340, S.342, D.343, R.346 Chain B: L.759, S.760 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.340, A:R.346, B:S.760, B:S.760 Water bridges: A:S.342, A:S.342, B:E.279

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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