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1l3h

NMR structure of P41icf, a potent inhibitor of human cathepsin L

Method: SOLUTION NMR Dmax: 32.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT (P41icf)

OrganismNot specified

UniProt P04233

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 210–274 Fragment：THYROGLOBULIN-LIKE DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.7；288 K；Pressure ambient NMR sample composition：1mM P41icf; 20mM phosphate buffer, 0.01mM NaN3 | 85% H20, 15% 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 1L3H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A6A THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3 Deposited 1998-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 103–117（15 aa） Fragment：CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5
Resolution 2.75 Å R-free 0.325
1A6A THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3 Deposited 1998-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 103–117（15 aa） Fragment：CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5
Resolution 2.75 Å R-free 0.325
1ICF CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L Deposited 1999-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 210–274（65 aa） Fragment：THYROGLOBULIN TYPE-1 DOMAIN
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；SITTING DROP VAPOR DIFFUSION METHOD RESERVOIR CONTAINED 1ML OF 0.2 M NA- ACETATE TRIHYDRATE, 30% W/V PEG 8K AND 0.1M MES, PH 6.1. DROP WAS COMPOSED OF 2 MICRO L OF RESERVOIR SOLUTION AND 2 MICRO L OF THE COMPLEX (10 MG/ML) IN 20MM NA-ACETATE AND 1MM EDTA, PH 5.0.
Resolution 2.00 Å R-free 0.213
1ICF CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L Deposited 1999-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 210–274（65 aa） Fragment：THYROGLOBULIN TYPE-1 DOMAIN
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；SITTING DROP VAPOR DIFFUSION METHOD RESERVOIR CONTAINED 1ML OF 0.2 M NA- ACETATE TRIHYDRATE, 30% W/V PEG 8K AND 0.1M MES, PH 6.1. DROP WAS COMPOSED OF 2 MICRO L OF RESERVOIR SOLUTION AND 2 MICRO L OF THE COMPLEX (10 MG/ML) IN 20MM NA-ACETATE AND 1MM EDTA, PH 5.0.
Resolution 2.00 Å R-free 0.213
1ICF CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L Deposited 1999-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 210–274（65 aa） Fragment：THYROGLOBULIN TYPE-1 DOMAIN
Chain J 210–274（65 aa） Fragment：THYROGLOBULIN TYPE-1 DOMAIN
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；SITTING DROP VAPOR DIFFUSION METHOD RESERVOIR CONTAINED 1ML OF 0.2 M NA- ACETATE TRIHYDRATE, 30% W/V PEG 8K AND 0.1M MES, PH 6.1. DROP WAS COMPOSED OF 2 MICRO L OF RESERVOIR SOLUTION AND 2 MICRO L OF THE COMPLEX (10 MG/ML) IN 20MM NA-ACETATE AND 1MM EDTA, PH 5.0.
Resolution 2.00 Å R-free 0.213
1IIE HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN Deposited 1999-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 118–192（75 aa） Fragment：ECTOPLASMIC TRIMERIZATION DOMAIN (RESIDUES 118-192)
Chain B 118–192（75 aa） Fragment：ECTOPLASMIC TRIMERIZATION DOMAIN (RESIDUES 118-192)
Chain C 118–192（75 aa） Fragment：ECTOPLASMIC TRIMERIZATION DOMAIN (RESIDUES 118-192)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Pressure 1
Resolution not provided
3PDO Crystal Structure of HLA-DR1 with CLIP102-120 Deposited 2010-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 102–120（19 aa）
Not recorded GOL GLYCEROL × 2 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350, NaCitrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å R-free 0.240
3PGC Crystal Structure of HLA-DR1 with CLIP106-120, flipped peptide orientation Deposited 2010-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 106–120（15 aa） Fragment：UNP residues 106-120
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 1500, MIB buffer, pH 6.0, vapor diffusion, sitting drop, temperature 298K
Resolution 2.66 Å R-free 0.250
3PGC Crystal Structure of HLA-DR1 with CLIP106-120, flipped peptide orientation Deposited 2010-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 106–120（15 aa） Fragment：UNP residues 106-120
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 1500, MIB buffer, pH 6.0, vapor diffusion, sitting drop, temperature 298K
Resolution 2.66 Å R-free 0.250
3PGD Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation Deposited 2010-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 106–120（15 aa） Fragment：UNP residues 106-120
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, NaCitrate, BisTris propane, pH 6.5, vapor diffusion, sitting drop, temperature 277K
Resolution 2.72 Å R-free 0.242
3PGD Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation Deposited 2010-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 106–120（15 aa） Fragment：UNP residues 106-120
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, NaCitrate, BisTris propane, pH 6.5, vapor diffusion, sitting drop, temperature 277K
Resolution 2.72 Å R-free 0.242
3QXA HLA-DR1 bound with CLIP peptide Deposited 2011-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 103–117（15 aa） Fragment：CLIP region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, 10% Glycerol, 100mM Sodium Acetate pH 5.6, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.71 Å R-free 0.235
3QXA HLA-DR1 bound with CLIP peptide Deposited 2011-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 103–117（15 aa） Fragment：CLIP region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, 10% Glycerol, 100mM Sodium Acetate pH 5.6, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.71 Å R-free 0.235
3QXD F54C HLA-DR1 bound with CLIP peptide Deposited 2011-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 103–117（15 aa） Fragment：CLIP region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, 10% Glycerol, 100mM Sodium Acetate pH 5.6, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
3QXD F54C HLA-DR1 bound with CLIP peptide Deposited 2011-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 103–117（15 aa） Fragment：CLIP region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, 10% Glycerol, 100mM Sodium Acetate pH 5.6, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
4AEN HLA-DR1 with covalently linked CLIP106-120 in reversed orientation Deposited 2012-01-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 106–120（15 aa） Fragment：RESIDUES 106-120
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 2 M (NH4)2SO4, 0.1 M TRIS, PH 8.0
Resolution 2.20 Å R-free 0.221
4AH2 HLA-DR1 with covalently linked CLIP106-120 in canonical orientation Deposited 2012-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 106–120（15 aa） Fragment：EXTRACELLULAR DOMAIN, RESIDUES 106-120,30-227
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.2 M LICL, 20% (W/V) PEG6000, 0.1 M HEPES, PH 7.0
Resolution 2.36 Å R-free 0.240
4X5W HLA-DR1 with CLIP102-120(M107W) Deposited 2014-12-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 102–120（19 aa） Fragment：extracellular, UNP residues 102-120
Mutation：M107W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M K/Na-tartrate, 20% (w/v) PEG3350, 0.1M BisTrisPropane, pH 8.5
Resolution 1.34 Å R-free 0.170
8VRW Cryo-EM structure of human invariant chain in complex with HLA-DR15 Deposited 2024-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 2–296（295 aa）
Chain F 2–296（295 aa）
Chain I 2–296（295 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
8VSJ Engineered peptide-specific binder in complex with HLA-DR1/CLIP Deposited 2024-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 103–117（15 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8VSP Cryo-EM structure of human invariant chain in complex with HLA-DQ Deposited 2024-01-24 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 × 9 PDB declaration: nonameric
Chain C 2–296（295 aa）
Chain F 2–296（295 aa）
Chain I 2–296（295 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9CYL Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 103–117（15 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293.15 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350
Resolution 4.66 Å R-free 0.326
9CYM Structure of LAG3 bound to the MHC class II molecule I-A(b) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 103–117（15 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.15 M Ammonium sulfate, 0.1 M Tris 8.0 and 15 % w/v PEG 4000
Resolution 3.84 Å R-free 0.307
9EJH Peptide-independent T cell receptor recognition of HLA-DQ2 Deposited 2024-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 110–122（13 aa） Fragment：UNP residues 110-122
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ACT ACETATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% Tacsimate, pH 8.0, 20-24% w/v PEG3350
Resolution 2.45 Å R-free 0.232

17 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HG2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–65； UniProt 210–274

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 1l3h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l3h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l3h
Deposition date deposition_date2002-02-27
Structure title titleNMR structure of P41icf, a potent inhibitor of human cathepsin L
Keywords keywordsALPHA HELIX, BETA SHEET, DISULFIDE BONDS, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.32 Å
Radius of gyration Rg (electron density) rg_electron11.45 Å
Forward intensity I(0) i0779405000.00
Molecular weight molecular_weight217020.0 kDa
Excluded volume excluded_volume262690 ų
Envelope volume envelope_volume15309 ų
Hydration-shell volume shell_volume10237 ų
Envelope diameter envelope_diameter42.7 Å
Shell Rg shell_rg18.45 Å
Envelope Rg envelope_rg13.17 Å
Shape Rg shape_rg11.45 Å
Total Rg total_rg11.53 Å
Total atoms total_atoms28950
Residues n_residues1950
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 dmax32.3 Å
Rg (real space) rg_real11.26 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real7.7940e+08
I(0) uncertainty (real space) i0_real_error7.8280e+06
Rg (reciprocal space) rg_reciprocal11.27 Å
I(0) (reciprocal space) i0_reciprocal779400000.0000
Solution quality estimate total_estimate0.8463
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.023
Kurtosis Kurtosis kurtosis-0.749
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38640.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1l3ha_
Class classg — Small proteins
Fold Fold foldg.28 — Thyroglobulin type-1 domain
Superfamily Superfamily superfamilyg.28.1 — Thyroglobulin type-1 domain
Family Family familyg.28.1.1 — Thyroglobulin type-1 domain

CATH v4.4 (1 domains)

Domain ID domain_id1l3hA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology800 — Invariant Chain; Chain I
Homologous superfamily homologous superfamily10 — Thyroglobulin type-1
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8. Citations (1)

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9. Files and Curves (10)