SMTL ID : 7vc7.1

The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

monomer

Ligands

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

1PE.1: 11 residues within 4Å: Chain A: Y.153, A.156, Q.157, Y.160, P.216, S.220, E.670, L.671, V.672, S.696, R.706 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.670 1PE.6: 2 residues within 4Å: Chain A: S.384, R.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.384, A:R.386 1PE.8: 10 residues within 4Å: Chain A: P.395, Q.402, N.432, T.434, A.435, S.442, G.443, S.446 Ligands: 1PE.9, NAG.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.402, A:N.432, A:S.446 1PE.9: 3 residues within 4Å: Chain A: T.466 Ligands: 1PE.8, NAG.24 No protein-ligand interaction detected (PLIP) 1PE.10: 6 residues within 4Å: Chain A: T.441, F.444, D.485, E.488, Q.489, A.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.489 1PE.11: 5 residues within 4Å: Chain A: T.401, Q.402, D.464, E.465, H.472 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.402 1PE.12: 6 residues within 4Å: Chain A: E.478, S.510, A.556, A.557, V.559, D.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.510, A:D.560 1PE.13: 9 residues within 4Å: Chain A: L.484, E.488, A.491, S.511, L.512, S.515, K.516, A.517, V.518 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.511, A:S.515, A:K.516 1PE.14: 3 residues within 4Å: Chain A: K.513, A.514, V.588 No protein-ligand interaction detected (PLIP) 1PE.15: 4 residues within 4Å: Chain A: K.642, S.644, G.645, G.683 No protein-ligand interaction detected (PLIP) 1PE.16: 6 residues within 4Å: Chain A: I.205, T.207, V.237, N.238, Y.247, P.742 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.207 1PE.17: 3 residues within 4Å: Chain A: D.378, G.379, K.646 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.646, A:K.646

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

PEG.2: 4 residues within 4Å: Chain A: D.255, H.256, G.258, F.628 No protein-ligand interaction detected (PLIP) PEG.3: 2 residues within 4Å: Chain A: W.193, D.560 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.574 PEG.5: 1 residues within 4Å: Chain A: K.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.388 PEG.7: 3 residues within 4Å: Chain A: L.383, S.384, R.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.385 PEG.18: 2 residues within 4Å: Chain A: P.555, T.586 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.586

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

EDO.4: 3 residues within 4Å: Chain A: N.196, F.201, N.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202

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

NAG.19: 1 residues within 4Å: Chain A: N.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.17 NAG.20: 3 residues within 4Å: Chain A: E.36, E.37, N.40 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.36 NAG.21: 1 residues within 4Å: Chain A: N.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.74 NAG.22: 1 residues within 4Å: Chain A: N.279 No protein-ligand interaction detected (PLIP) NAG.23: 3 residues within 4Å: Chain A: N.398, T.400, F.430 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.430 Hydrogen bonds: A:N.398, A:T.400, A:T.400 NAG.24: 4 residues within 4Å: Chain A: F.430, N.432 Ligands: 1PE.8, 1PE.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.430 NAG.25: 5 residues within 4Å: Chain A: N.437, I.467, S.476, E.478, P.480 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.480

1 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.26: 13 residues within 4Å: Chain A: W.60, E.62, F.129, R.143, K.183, H.184, R.198, M.231, Y.234, D.267, C.268, Y.407, E.470 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.143, A:R.143, A:K.183, A:K.183, A:H.184, A:R.198, A:Y.234, A:Y.234, A:Y.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kojima, K. et al., Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J.Biol.Chem. (2022)

Release Date

2022-02-09

Peptides

xylan 1,4-beta-xylosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

xylan 1,4-beta-xylosidase