34RH | pdb_000034rh

Trametes ljubarski GH12 endoglucanase bound to xyloglucan (XXXG)

PDB DOI: https://doi.org/10.2210/pdb34RH/pdb

Classification: HYDROLASE
Organism(s): Pilatotrama ljubarskyi
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2026-09-28 Released: 2026-10-28
Deposition Author(s): Correa, T.L.R., McGregor, N.G.S., de Boer, C., Schroder, S.P., Foucart, Q., Moroz, O., Willems, L.I., Berrin, J.-G., Faure, R., Overkleeft, H.S., Davies, G.J.D.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.239 (Depositor), 0.249 (DCC)
R-Value Work:
0.211 (Depositor), 0.219 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Complementary chemical probes and substrates reveal split subsite specificity in a fungal GH12 glucanase

Correa, T.L.R., McGregor, N.G.S., de Boer, C., Schroder, S.P., Foucart, Q., Moroz, O., Willems, L.I., Berrin, J.-G., Faure, R., Overkleeft, H.S., Davies, G.J.

To be published.

Macromolecule Content

Total Structure Weight: 27.2 kDa
Atom Count: 1,896
Modeled Residue Count: 227
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH12 endoglucanase	A	235	Pilatotrama ljubarskyi	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	5		N/A	Interactions Focus chain B Interactions & Density Focus chain B

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYS (Subject of Investigation/LOI) Query on XYS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	alpha-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-LECHCGJUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.239 (Depositor), 0.249 (DCC)
R-Value Work: 0.211 (Depositor), 0.219 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.95	α = 90
b = 149.41	β = 90
c = 50.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

McGregor, N.G.S.

Overkleeft, H.S.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	ERC-2020-SyG-951231

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release