9FNL | pdb_00009fnl

The structure of CBM42 from Clostridium thermocellum in complex with arabinofuranosyl xylobiose (A3X) substrate molecules

PDB DOI: https://doi.org/10.2210/pdb9FNL/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Acetivibrio thermocellus DSM 1313
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-10 Released: 2025-06-25
Deposition Author(s): Hadad, N., Lavid, N., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.212 (Depositor), 0.211 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The structure of CBM42 from Clostridium thermocellum in complex with arabinofuranosyl xylobiose (A3X) substrate molecules

Hadad, N., Lavid, N., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 102.73 kDa
Atom Count: 8,102
Modeled Residue Count: 804
Deposited Residue Count: 810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-sigma-I factor RsgI5	A, B, C, D, E A, B, C, D, E, F	135	Acetivibrio thermocellus DSM 1313	Mutation(s): 0 Gene Names: rsgI5, Cthe_1273
UniProt
Find proteins for A3DEX6 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DEX6 Go to UniProtKB: A3DEX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DEX6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	G, H [auth I], I [auth J], J [auth K], K [auth L], G, H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth T]	3		N/A	Interactions Focus chain G Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth T] Interactions & Density Focus chain G Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth T]
Glycosylation Resources
GlyTouCan: G96828DL GlyCosmos: G96828DL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth E] MOL2 format, chain DA [auth E] mmCIF format, chain DA [auth E]	DA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Interactions & Density Focus chain DA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth A] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] EA [auth E] FA [auth E] AA [auth D], BA [auth D], CA [auth D], EA [auth E], FA [auth E], GA [auth F], HA [auth F], S [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]