8H2W

Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines

PDB DOI: https://doi.org/10.2210/pdb8H2W/pdb

Classification: CARBOHYDRATE
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-10-07 Released: 2023-10-11
Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.163
R-Value Work: 0.143
R-Value Observed: 0.144

wwPDB Validation 3D Report Full Report

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

Literature

11 cysteine-to-serine mutations improve stability of cellodextrin phosphorylase from Clostridium thermocellum

Kuga, T., Sunagawa, N., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 230.34 kDa
Atom Count: 19,208
Modelled Residue Count: 1,968
Deposited Residue Count: 1,986
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellodextrin phosphorylase	A, B	993	Acetivibrio thermocellus	Mutation(s): 12 Gene Names: cdp-ym4
UniProt
Find proteins for Q93HT8 (Acetivibrio thermocellus) Explore Q93HT8 Go to UniProtKB: Q93HT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93HT8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	3		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G14338VK GlyCosmos: G14338VK GlyGen: G14338VK

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain EA [auth B] SDF format, chain G [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain G [auth A]	BA [auth B], EA [auth B], G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth B] Focus chain EA [auth B] Focus chain G [auth A] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth B] Focus chain G [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	HA [auth B], IA [auth B], L [auth A], M [auth A], N [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain K [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain K [auth A]	GA [auth B], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth B] Focus chain K [auth A] Interactions & Density Focus chain GA [auth B] Focus chain K [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain TA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	JA [auth B] KA [auth B] LA [auth B] MA [auth B] NA [auth B] JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A], Y [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	CA [auth B] DA [auth B] E [auth A] F [auth A] FA [auth B] CA [auth B], DA [auth B], E [auth A], F [auth A], FA [auth B], H [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain XA [auth B] SDF format, chain AA [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain Z [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain Z [auth A]	AA [auth A], VA [auth B], WA [auth B], XA [auth B], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Z [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021 Query on PRD_900021	C, D	beta-cellotriose	Oligosaccharide / Metabolism		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D