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6ve1

Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH

Method: X-RAY DIFFRACTION Dmax: 93.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endo-beta-N-acetylglucosaminidase H

Streptomyces plicatus

UniProt P04067

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 47–313 Chain D； UniProt 47–313 Fragment：UNP residues 47-313 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0 Resolution 2.10 Å R-free 0.258
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 47–313 Chain C； UniProt 47–313 Fragment：UNP residues 47-313 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0 Resolution 2.10 Å R-free 0.258

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 6VE1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C3F Endo-Beta-N-Acetylglucosaminidase H, D130N Mutant Deposited 1999-07-27 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 48–312（265 aa）
Mutation：D130N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG8000, 200 MM ZINC ACETATE 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.10 Å
1C8X Endo-Beta-N-Acetylglucosaminidase H, D130E Mutant Deposited 1999-07-30 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 48–312（265 aa）
Mutation：D130E PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；30% PEG1000, 100 MM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.00 Å
1C8Y Endo-Beta-N-Acetylglucosaminidase H, D130A Mutant Deposited 1999-07-30 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 48–312（265 aa）
Mutation：D130A ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG1000, 100 MM ZN(AC)2, 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30 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 48–312（265 aa）
Mutation：E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 48–312（265 aa）
Mutation：E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C91 Endo-Beta-N-Acetylglucosaminidase H, E132D Deposited 1999-07-30 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 48–312（265 aa）
Mutation：E132D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C92 Endo-Beta-N-Acetylglucosaminidase H, E132A Mutant Deposited 1999-07-30 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 48–312（265 aa）
Mutation：E132A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；24% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C93 Endo-Beta-N-Acetylglucosaminidase H, D130N/E132Q Double Mutant Deposited 1999-07-30 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 48–312（265 aa）
Mutation：D130N AND E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；34% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1EDT CRYSTAL STRUCTURE OF ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H AT 1.9 ANGSTROMS RESOLUTION: ACTIVE SITE GEOMETRY AND SUBSTRATE RECOGNITION Deposited 1995-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–313（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28 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 48–312（265 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)
Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 48–312（265 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)
Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 48–312（265 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)
Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 48–312（265 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)
Resolution 1.99 Å R-free 0.261

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EBAG_STRPL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–275； UniProt 47–313 Author chain B； PDBConstruct 9–275； UniProt 47–313 Author chain C； PDBConstruct 9–275； UniProt 47–313 Author chain D； PDBConstruct 9–275； UniProt 47–313

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 6ve1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ve1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ve1
Deposition date deposition_date2019-12-28
Structure title titleCrystal structure of endo-beta-N-acetylglucosaminidase H at high pH
Keywords keywordsenzyme, deglycosylase, post-translational modification, HYDROLASE, SUGAR BINDING PROTEIN; HYDROLASE, SUGAR BINDING PROTEIN
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_guinier32.08 Å
Radius of gyration Rg (electron density) rg_electron30.93 Å
Forward intensity I(0) i0214901000.00
Molecular weight molecular_weight114810.0 kDa
Excluded volume excluded_volume142550 ų
Envelope volume envelope_volume174390 ų
Hydration-shell volume shell_volume45532 ų
Envelope diameter envelope_diameter96.9 Å
Shell Rg shell_rg39.45 Å
Envelope Rg envelope_rg30.45 Å
Shape Rg shape_rg30.89 Å
Total Rg total_rg31.76 Å
Total atoms total_atoms15884
Residues n_residues1069
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 dmax93.9 Å
Rg (real space) rg_real31.83 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real2.1490e+08
I(0) uncertainty (real space) i0_real_error2.8220e+06
Rg (reciprocal space) rg_reciprocal31.94 Å
I(0) (reciprocal space) i0_reciprocal214900000.0000
Solution quality estimate total_estimate0.9034
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.2 Å
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35210000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.833
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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) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd6ve1a_
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.1.8.5 — Type II chitinase
Domain ID domain_idd6ve1b1
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.1.8.5 — Type II chitinase
Domain ID domain_idd6ve1b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6ve1c1
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.1.8.5 — Type II chitinase
Domain ID domain_idd6ve1c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6ve1d1
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.1.8.5 — Type II chitinase
Domain ID domain_idd6ve1d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)