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1hm2

ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS

Method: X-RAY DIFFRACTION Dmax: 97.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CHONDROITINASE AC

Pedobacter heparinus

UniProt Q59288

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 3 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–700 Not recorded ;2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose ; × 1 alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose × 1 ;alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose ; × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 3350, sodium acetate, hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.00 Å R-free 0.270

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 1HM2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CB8 CHONDROITINASE AC LYASE FROM FLAVOBACTERIUM HEPARINUM Deposited 1999-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–700（678 aa）
Not recorded CA CALCIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；CRYSTALLIZATION CONDITIONS: PEG-MME 2K 17% AMMONIUM ACETATE 80MM PH 6.5 0.4M SODIUM ACETATE
Resolution 1.90 Å R-free 0.260
1HM3 ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS Deposited 2000-12-04 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–700（700 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 3350, sodium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.254
1HMU ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS Deposited 2000-12-05 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–700（700 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 3350, sodium acetate, hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.00 Å R-free 0.266
1HMW ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS Deposited 2000-12-05 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–700（700 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 3350, sodium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.275

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHAC_PEDHE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–700； UniProt 1–700

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 1hm2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hm2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hm2
Deposition date deposition_date2000-12-04
Structure title titleACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS
Keywords keywordsprotein-oligosaccharide complex, active site, catalysis, LYASE; LYASE
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_guinier28.05 Å
Radius of gyration Rg (electron density) rg_electron27.46 Å
Forward intensity I(0) i097028700.00
Molecular weight molecular_weight78317.0 kDa
Excluded volume excluded_volume98185 ų
Envelope volume envelope_volume115900 ų
Hydration-shell volume shell_volume35189 ų
Envelope diameter envelope_diameter102.5 Å
Shell Rg shell_rg34.95 Å
Envelope Rg envelope_rg27.76 Å
Shape Rg shape_rg27.43 Å
Total Rg total_rg28.29 Å
Total atoms total_atoms5530
Residues n_residues674
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 dmax97.5 Å
Rg (real space) rg_real28.10 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real9.7030e+07
I(0) uncertainty (real space) i0_real_error1.5710e+06
Rg (reciprocal space) rg_reciprocal28.08 Å
I(0) (reciprocal space) i0_reciprocal97030000.0000
Solution quality estimate total_estimate0.8567
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5 Å
Skewness Skewness skewness0.451
Kurtosis Kurtosis kurtosis-0.160
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19510000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.977
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1hm2a1
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.3 — Chondroitin AC/alginate lyase
Family Family familya.102.3.2 — Hyaluronate lyase-like catalytic, N-terminal domain
Domain ID domain_idd1hm2a2
Class classb — All beta proteins
Fold Fold foldb.24 — Hyaluronate lyase-like, C-terminal domain
Superfamily Superfamily superfamilyb.24.1 — Hyaluronate lyase-like, C-terminal domain
Family Family familyb.24.1.1 — Hyaluronate lyase-like, C-terminal domain
Domain ID domain_idd1hm2a3
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.2 — Hyaluronate lyase-like, central domain

CATH v4.4 (3 domains)

Domain ID domain_id1hm2A01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily100 — Chondroitin AC/alginate lyase
Domain ID domain_id1hm2A02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1hm2A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Polysaccharide lyase family 8-like, C-terminal
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8. Citations (1)

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9. Files and Curves (10)