5A7M
The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1)
- PDB DOI: https://doi.org/10.2210/pdb5A7M/pdb
- Classification: HYDROLASE
- Organism(s): Trichoderma reesei
- Expression System: Trichoderma reesei
- Mutation(s): No 
- Deposited: 2015-07-08 Released: 2016-08-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.199 
- R-Value Work: 0.161 
- R-Value Observed: 0.162 
This is version 3.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
BETA-XYLOSIDASE | 766 | Trichoderma reesei | Mutation(s): 0  EC: 3.2.1.37 | ||
UniProt | |||||
Find proteins for Q92458 (Hypocrea jecorina) Explore Q92458  Go to UniProtKB:  Q92458 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q92458 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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 | C | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G07617FP GlyCosmos:  G07617FP GlyGen:  G07617FP |
Entity ID: 3 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, F, J, K | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | E, I | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42227JK GlyCosmos:  G42227JK GlyGen:  G42227JK |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 6 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | H | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | EA [auth B] FA [auth B] GA [auth B] L [auth A] M [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
TRS Query on TRS | AA [auth A], BA [auth A], SA [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
GOL Query on GOL | CA [auth A], TA [auth B], UA [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | HA [auth B] IA [auth B] JA [auth B] KA [auth B] LA [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
ACT Query on ACT | DA [auth A], VA [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | A, B | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.199 
- R-Value Work: 0.161 
- R-Value Observed: 0.162 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 99.911 | α = 90 |
b = 203.724 | β = 90 |
c = 82.112 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
TRUNCATE | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-08-10  Deposition Author(s): Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Hansson, H., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T.
Revision History (Full details and data files)
- Version 1.0: 2016-08-10
Type: Initial release - Version 1.1: 2018-01-17
Changes: Data collection - Version 2.0: 2020-03-11
Changes: Data collection, Derived calculations, Other, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary