6K54

Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with trisaccharide

PDB DOI: https://doi.org/10.2210/pdb6K54/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-28 Released: 2020-06-03
Deposition Author(s): Baba, S., Takeda, M., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.201
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 144.54 kDa
Atom Count: 11,798
Modelled Residue Count: 1,284
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH6 cellobiohydrolase, HMCEL6A	A, B, C	428	metagenome	Mutation(s): 0 EC: 3.2.1.91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	4		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G41724ZD GlyCosmos: G41724ZD GlyGen: G41724ZD

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B]	M [auth A], U [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth C]	N [auth A], O [auth A], Z [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth C] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	J [auth A] K [auth A] S [auth B] T [auth B] X [auth C] J [auth A], K [auth A], S [auth B], T [auth B], X [auth C], Y [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	H [auth A] I [auth A] P [auth B] Q [auth B] R [auth B] H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.201
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.582	α = 90
b = 138.699	β = 101.99
c = 110.636	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary