5AE6

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) in complex with 4-thioxylobiose

PDB DOI: https://doi.org/10.2210/pdb5AE6/pdb

Classification: HYDROLASE
Organism(s): Trichoderma reesei
Mutation(s): No

Deposited: 2015-08-26 Released: 2016-09-21
Deposition Author(s): Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Hansson, H., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.214 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Th Crystal Structure of a Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, Xyl3A from Hypocrea Jecorina

Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T., Hansson, H.

To be published.

Macromolecule Content

Total Structure Weight: 176.48 kDa
Atom Count: 13,404
Modelled Residue Count: 1,529
Deposited Residue Count: 1,534
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-XYLOSIDASE	A, B	767	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
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 2
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	C	4		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
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, H, I, K	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain H Focus chain I Focus chain K Interactions & Density Focus chain D Focus chain F Focus chain H Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-4-deoxy-4-thio-alpha-D-xylopyranose	G, L	2	N/A	N/A	Interactions Focus chain G Focus chain L Interactions & Density Focus chain G Focus chain L
Glycosylation Resources
GlyTouCan: G58687LH GlyCosmos: G58687LH

Entity ID: 6
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	J	5		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] M [auth A] N [auth A] O [auth A] P [auth A] AA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]

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: 2.10 Å
R-Value Free: 0.214 (Depositor), 0.210 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.244	α = 90
b = 202.443	β = 90
c = 82.441	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-21
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
Version 3.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-11-06
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5AE6

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) in complex with 4-thioxylobiose

Th Crystal Structure of a Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, Xyl3A from Hypocrea Jecorina

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)