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4u5k

Complex structure of mutant CtCel5E (E314A) with cellobiose

Method: X-RAY DIFFRACTION Dmax: 88.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endoglucanase H

Clostridium thermocellum ATCC 27405

UniProt P16218

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 290–654 Fragment：UNP residues 290-654 Mutation：E314A beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2M ammonium acetate, 0.1M sodium acetate, 21% (W/V) PEG 4000 Resolution 2.65 Å R-free 0.255
2 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 290–654 Fragment：UNP residues 290-654 Mutation：E314A beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2M ammonium acetate, 0.1M sodium acetate, 21% (W/V) PEG 4000 Resolution 2.65 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4U5K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1V0A Family 11 Carbohydrate-Binding Module of cellulosomal cellulase Lic26A-Cel5E of Clostridium thermocellum Deposited 2004-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 655–821（167 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.00
Resolution 1.98 Å R-free 0.232
2BV9 HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CtLIC26A Deposited 2005-06-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–304（279 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-304
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.3-1.2M NA FORMATE, 0.1M NA CACODYLATE BUFFERED AT PH 6.5 AND 5-20% PEG 4K
Resolution 1.50 Å R-free 0.157
2BVD HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CtLIC26A Deposited 2005-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–304（279 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-304
Not recorded ISX (3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)piperidin-3-yl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CO-CRYSTALLIZED WITH THE LIGAND FROM 0.15 M AMMONIUM SULPHATE, 30% PEG 5K MME BUFFERED TO PH 6.5 WITH MES
Resolution 1.60 Å R-free 0.186
2CIP Structure of the Michaelis complex of a family 26 lichenase Deposited 2006-03-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–304（279 aa） Fragment：RESIDUES 26-304
Mutation：YES ZZ1 4-METHYL-2H-CHROMEN-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.15 M AMMONIUM SULPHATE, 30 % PEG 5K MME BUFFERED TO PH6.5 WITH 0.1 M MES, pH 6.50
Resolution 1.40 Å R-free 0.179
2CIT Structure of the covalent intermediate of a family 26 lichenase Deposited 2006-03-24 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–304（279 aa） Fragment：RESIDUES 26-304
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.15 M AMMONIUM SULPHATE, 30 % PEG 5K MME BUFFERED TO PH 6.5 WITH 0.1 M MES
Resolution 1.40 Å R-free 0.179
2LRO Solution structure, dynamics and binding studies of CtCBM11 Deposited 2012-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 655–821（167 aa） Fragment：CBM11 domain residues 655-821
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.75；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N] protein_1, 0.75 mM potassium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LRP Solution structure, dynamics and binding studies of CtCBM11 Deposited 2012-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 655–821（167 aa） Fragment：CBM11 domain residues 655-821
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；323 K；Ionic strength (raw mmCIF value) 0.75；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N] protein_1, 0.75 mM potassium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2V3G Structure of a family 26 lichenase in complex with noeuromycin Deposited 2007-06-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–305（280 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-305
Not recorded BGC beta-D-glucopyranose × 1 NOY (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；CO-CRYSTALLIZED WITH THE LIGAND FROM 0.15 M AMMONIUM SULPHATE, 30% PEG 5K MME BUFFERED TO PH 6.5 WITH MES AND SEEDED
Resolution 1.20 Å R-free 0.144
2VI0 Lichenase CtLic26 in complex with a thio-oligosaccharide Deposited 2007-11-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–304（279 aa） Fragment：RESIDUES 26-304
Mutation：G271E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.15 M AMMONIUM SULPHATE, 30 % PEG 5K, MME, 0.1 M MES PH 6.5
Resolution 1.51 Å R-free 0.189
4U3A Crystal structure of CtCel5E Deposited 2014-07-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate and 21% (W/V) PEG 4000
Resolution 2.42 Å R-free 0.248
4U3A Crystal structure of CtCel5E Deposited 2014-07-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate and 21% (W/V) PEG 4000
Resolution 2.42 Å R-free 0.248
4U5I Complex structure of mutant CtCel5E (E314A) with xylobiose Deposited 2014-07-25 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 290–654（365 aa） Fragment：UNP residues 290-654
Mutation：E314A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium acetate, 0.1 M sodium acetate and 21% (W/V) PEG 4000
Resolution 2.50 Å R-free 0.252
4U5I Complex structure of mutant CtCel5E (E314A) with xylobiose Deposited 2014-07-25 Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 290–654（365 aa） Fragment：UNP residues 290-654
Mutation：E314A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.2 M ammonium acetate, 0.1 M sodium acetate and 21% (W/V) PEG 4000
Resolution 2.50 Å R-free 0.252
5BYW Crystal structure of engineered trifunctional CtCEL5E Deposited 2015-06-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；50mM sodium acetate, 8% PEG 4000
Resolution 2.60 Å R-free 0.260
5BYW Crystal structure of engineered trifunctional CtCEL5E Deposited 2015-06-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；50mM sodium acetate, 8% PEG 4000
Resolution 2.60 Å R-free 0.260
5BYW Crystal structure of engineered trifunctional CtCEL5E Deposited 2015-06-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；50mM sodium acetate, 8% PEG 4000
Resolution 2.60 Å R-free 0.260
5BYW Crystal structure of engineered trifunctional CtCEL5E Deposited 2015-06-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；50mM sodium acetate, 8% PEG 4000
Resolution 2.60 Å R-free 0.260
5BYW Crystal structure of engineered trifunctional CtCEL5E Deposited 2015-06-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 290–654（365 aa） Fragment：UNP residues 290-654
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；50mM sodium acetate, 8% PEG 4000
Resolution 2.60 Å R-free 0.260
6R31 Family 11 Carbohydrate-Binding Module from Clostridium thermocellum in complex with beta-1,3-1,4-mixed-linked tetrasaccharide Deposited 2019-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 655–821（167 aa）
Not recorded CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；20-28% (m/v) polyethyleneglycol (PEG) 3350, 0.2 M potassium phosphate, 0.1 M sodium acetate buffer pH 4.6
Resolution 2.60 Å R-free 0.254
6R3M Family 11 Carbohydrate-Binding Module from Clostridium thermocellum in complex with beta-1,3-1,4-mixed-linked tetrasaccharide Deposited 2019-03-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 655–821（167 aa）
Not recorded CA CALCIUM ION × 2 ACT ACETATE ION × 1 PO4 PHOSPHATE ION × 4 GLC alpha-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；20-28% (m/v) polyethyleneglycol (PEG) 3350, 0.2 M potassium phosphate, 0.1 M sodium acetate buffer pH 4.6
Resolution 1.45 Å R-free 0.208
6ZPL Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions. Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 31–303（273 aa）
Not recorded QET [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；292.75 K；Crystals appeared in 3-10 days in 0.1 M ADA pH 7, 13-25% PEG600, 4-14% v/v, 1,3-Butanediol with the longest dimension of 2-5 um.
Resolution 3.94 Å R-free 0.291
8XVI Cryo-EM structure of ETAR bound with Endothelin1 Deposited 2024-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 26–304（279 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8XVJ Cryo-EM structure of ETAR bound with Macitentan Deposited 2024-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 26–304（279 aa）
Not recorded A1D5I Macitentan × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
8XVK Cryo-EM structure of ETAR bound with Ambrisentan Deposited 2024-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 26–304（279 aa）
Not recorded A1D5J Ambrisentan × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8XVL Cryo-EM structure of ETAR bound with Zibotentan Deposited 2024-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 26–304（279 aa）
Not recorded A1D5L Zibotentan × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å

19 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GUNH_CLOTH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 39–403； UniProt 290–654 Author chain B； PDBConstruct 39–403； UniProt 290–654

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4u5k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4u5k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4u5k
Deposition date deposition_date2014-07-25
Structure title titleComplex structure of mutant CtCel5E (E314A) with cellobiose
Keywords keywordsbi-functional cellulase/xylanase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.94 Å
Radius of gyration Rg (electron density) rg_electron27.18 Å
Forward intensity I(0) i082115800.00
Molecular weight molecular_weight71410.0 kDa
Excluded volume excluded_volume89171 ų
Envelope volume envelope_volume102550 ų
Hydration-shell volume shell_volume31980 ų
Envelope diameter envelope_diameter90.5 Å
Shell Rg shell_rg34.30 Å
Envelope Rg envelope_rg26.99 Å
Shape Rg shape_rg27.14 Å
Total Rg total_rg28.00 Å
Total atoms total_atoms5051
Residues n_residues602
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.8 Å
Rg (real space) rg_real27.99 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real8.2120e+07
I(0) uncertainty (real space) i0_real_error1.1440e+06
Rg (reciprocal space) rg_reciprocal27.98 Å
I(0) (reciprocal space) i0_reciprocal82120000.0000
Solution quality estimate total_estimate0.8909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha32740000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.904
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4u5ka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches
Domain ID domain_idd4u5kb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id4u5kA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id4u5kB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)