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6kbv

Three-dimensional cytoplasmic membrane-bound structure of VG16KRKP-KYE28

Method: SOLUTION NMR Dmax: 40.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Heparin cofactor 2

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 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 192–219 Fragment：helix D VG16KRKP × 1 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

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 6KBV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JMJ Crystal Structure of Native Heparin Cofactor II Deposited 2001-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–499（480 aa）
Chain B 20–499（480 aa）
Not recorded 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
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 method 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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 experimental conditions 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 experimental conditions 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 oligomeric state Different experimental conditions 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 experimental conditions 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

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 2
Chains and sequence ranges Author chain B； PDBConstruct 1–28； UniProt 192–219

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 6kbv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6kbv
Deposition date deposition_date2019-06-26
Structure title titleThree-dimensional cytoplasmic membrane-bound structure of VG16KRKP-KYE28
Keywords keywordsantimicrobial peptide (AMP), antibiotic resistance, synergism, lipopolysaccharide (LPS), bacterial membrane, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier10.80 Å
Radius of gyration Rg (electron density) rg_electron10.73 Å
Forward intensity I(0) i083938800.00
Molecular weight molecular_weight79987.0 kDa
Excluded volume excluded_volume102150 ų
Envelope volume envelope_volume19332 ų
Hydration-shell volume shell_volume12256 ų
Envelope diameter envelope_diameter41.4 Å
Shell Rg shell_rg19.27 Å
Envelope Rg envelope_rg13.39 Å
Shape Rg shape_rg10.64 Å
Total Rg total_rg11.52 Å
Total atoms total_atoms11640
Residues n_residues660
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 dmax40.4 Å
Rg (real space) rg_real10.76 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real8.3940e+07
I(0) uncertainty (real space) i0_real_error1.0050e+06
Rg (reciprocal space) rg_reciprocal10.76 Å
I(0) (reciprocal space) i0_reciprocal83940000.0000
Solution quality estimate total_estimate0.8277
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.4 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.203
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha125500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.618; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)