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1hmw

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

Method: X-RAY DIFFRACTION Dmax: 96.8 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 ;4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-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 298K Resolution 2.30 Å R-free 0.275

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 1HMW 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
1HM2 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 2.00 Å R-free 0.270
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

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 1hmw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1hmw
Deposition date deposition_date2000-12-05
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_guinier28.08 Å
Radius of gyration Rg (electron density) rg_electron27.48 Å
Forward intensity I(0) i096908400.00
Molecular weight molecular_weight78282.0 kDa
Excluded volume excluded_volume98152 ų
Envelope volume envelope_volume117160 ų
Hydration-shell volume shell_volume35488 ų
Envelope diameter envelope_diameter101.8 Å
Shell Rg shell_rg35.03 Å
Envelope Rg envelope_rg27.77 Å
Shape Rg shape_rg27.44 Å
Total Rg total_rg28.32 Å
Total atoms total_atoms5528
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 dmax96.8 Å
Rg (real space) rg_real28.12 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real9.6910e+07
I(0) uncertainty (real space) i0_real_error1.5340e+06
Rg (reciprocal space) rg_reciprocal28.11 Å
I(0) (reciprocal space) i0_reciprocal96910000.0000
Solution quality estimate total_estimate0.8593
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.8 Å
Skewness Skewness skewness0.442
Kurtosis Kurtosis kurtosis-0.171
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19480000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.741; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.978
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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_idd1hmwa1
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_idd1hmwa2
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_idd1hmwa3
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_id1hmwA01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily100 — Chondroitin AC/alginate lyase
Domain ID domain_id1hmwA02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1hmwA03
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)