← Back to search
1jmj

Crystal Structure of Native Heparin Cofactor II

Method: X-RAY DIFFRACTION Dmax: 118.8 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

HEPARIN COFACTOR II

OrganismNot specified

UniProt P05546

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 Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 20–499 Chain B； UniProt 20–499 Not recorded beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；MgCl2, Tris, PEG 4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K Resolution 2.35 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 1JMJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JMO Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex Deposited 2001-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–499（480 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；NH4Cl, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.20 Å R-free 0.211
2NAT Structural insights into interaction of KYE28 and lipopolysachharide Deposited 2016-01-11 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 192–219（28 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 1 mM entity-1, 1 mM TSP-2, 55.5 mM H2O-3, 61.3 mM D2O-4, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NCU NMR structure of KYE21 in LPS micelles Deposited 2016-04-18 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 192–212（21 aa） Fragment：Glycosaminoglycan-binding site residues 192-212
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1 mM protein, 1 mM DSS, 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NCV NMR structure of RWS21 structure in LPS micelles Deposited 2016-04-18 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 192–212（21 aa） Fragment：Glycosaminoglycan-binding site residues 192-212
Mutation：L192R, Y193W, E194S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1 mM protein, 1 mM DSS, 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NCW NMR structure of WWWKYE21 structure in LPS micelles Deposited 2016-04-18 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 189–212（24 aa） Fragment：Glycosaminoglycan-binding site residues 189-212
Mutation：L192R, Y193W, E194S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1 mM protein, 1 mM DSS, 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6J12 Three-dimensional Solution NMR Structure of KYE28-PEG48 in Microgel Deposited 2018-12-27 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 192–219（28 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.52；298 K；Ionic strength (raw mmCIF value) 1；Pressure 9.8
NMR sample composition 1 mM KYE28-PEG48, 55.5 M Water, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KBO Three-dimensional LPS bound structure of VG16KRKP-KYE28. Deposited 2019-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 192–219（28 aa） Fragment：Helix-D
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.6；Pressure 1
NMR sample composition 0.3 mM 1H, Natural Abundance VG16KRKP, 0.3 mM 1H, Natural Abundance KYE28, 55.55 M 1H, Natural Abundance Water, 10 uM 1H, Natural Abundance Lipopolysaccharide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KBV Three-dimensional cytoplasmic membrane-bound structure of VG16KRKP-KYE28 Deposited 2019-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 192–219（28 aa） Fragment：helix D
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.6；Pressure 1
NMR sample composition 0.3 uM 1H, natural abundance VG16KRKP, 0.3 uM 1H, natural abundance KYE28, 12 uM 1H, natural abundance 3:1 POPE/POPG vesicles, 55.55 M 1H, natural abundance water, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEP2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–480； UniProt 20–499 Author chain B； PDBConstruct 1–480； UniProt 20–499

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 1jmj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jmj
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1jmj
Deposition date deposition_date2001-07-18
Structure title titleCrystal Structure of Native Heparin Cofactor II
Keywords keywordsserpin, THROMBIN INHIBITOR, HEPARIN, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.03 Å
Radius of gyration Rg (electron density) rg_electron33.99 Å
Forward intensity I(0) i0123193000.00
Molecular weight molecular_weight91447.0 kDa
Excluded volume excluded_volume115660 ų
Envelope volume envelope_volume140510 ų
Hydration-shell volume shell_volume36328 ų
Envelope diameter envelope_diameter123.9 Å
Shell Rg shell_rg38.15 Å
Envelope Rg envelope_rg34.00 Å
Shape Rg shape_rg33.98 Å
Total Rg total_rg34.34 Å
Total atoms total_atoms6426
Residues n_residues784
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax118.8 Å
Rg (real space) rg_real34.32 Å
Rg uncertainty (real space) rg_real_error1.38 Å
I(0) (real space) i0_real1.2320e+08
I(0) uncertainty (real space) i0_real_error2.2330e+06
Rg (reciprocal space) rg_reciprocal34.14 Å
I(0) (reciprocal space) i0_reciprocal123200000.0000
Solution quality estimate total_estimate0.7947
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis-0.263
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57740000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.635; Smooth: 0.731
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1jmja_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins
Domain ID domain_idd1jmjb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins

CATH v4.4 (4 domains)

Domain ID domain_id1jmjA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id1jmjA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
Domain ID domain_id1jmjB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id1jmjB02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
▶

8. Citations (1)

▶

9. Files and Curves (10)