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1icf

CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (CATHEPSIN L: HEAVY CHAIN)

OrganismNot specified

UniProt P07711

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 PROTEIN (INVARIANT CHAIN) × 1 （P04233） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 PROTEIN (INVARIANT CHAIN) × 1 （P04233） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 PROTEIN (INVARIANT CHAIN) × 2 （P04233） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1cjl 1cs8 2xu1 2xu1 2xu1 2xu1 2xu3 2xu4 2xu5 2yj2 2yj8 2yj9

132 assemblies; showing the first 12

Homodimer
3iv2 3iv2 4axl 5i4h 6ezx 8uac

6 assemblies

Homotetramer
2vhs 8b4f 8prx 8qkb

4 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1icf 1icf 1icf 1mhw 1mhw 2nqd 3k24 3k24 3kse 3kse 3kse 8a5b

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CATL_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–175； UniProt 114–288 Author chain C； PDBConstruct 1–175； UniProt 114–288 Author chain B； PDBConstruct 1–42； UniProt 292–333 Author chain D； PDBConstruct 1–42； UniProt 292–333

PROTEIN (INVARIANT CHAIN)

OrganismNot specified

UniProt P04233

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 PROTEIN (CATHEPSIN L: HEAVY CHAIN) × 1 （P07711） PROTEIN (CATHEPSIN L: LIGHT CHAIN) × 1 （P07711） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 PROTEIN (CATHEPSIN L: HEAVY CHAIN) × 1 （P07711） PROTEIN (CATHEPSIN L: LIGHT CHAIN) × 1 （P07711） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 PROTEIN (CATHEPSIN L: HEAVY CHAIN) × 2 （P07711） PROTEIN (CATHEPSIN L: LIGHT CHAIN) × 2 （P07711） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1l3h

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1iie

1 assemblies

Heteromeric or nucleic-acid complex
1a6a 1a6a 1icf 1icf 1icf 3pdo 3pgc 3pgc 3pgd 3pgd 3qxa 3qxa

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HG2A_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 1–65； UniProt 210–274 Author chain J； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1icf
Deposition date deposition_date1999-01-07
Structure title titleCRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L
Keywords keywordsCYSTEINE PROTEINASE, CATHEPSIN, MHC CLASS II, INVARIANT CHAIN, THYROGLOBULIN TYPE-1 DOMAIN, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1icf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1icf__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1icf__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）19.86 Å
Rg (electron density)18.94 Å
Total Rg19.88 Å
Atom count2196
Residues282
Excluded volume38350 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1icf__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1icf__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1icf__assembly_3__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1icf.1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like
Domain ID domain_idd1icf.2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like
Domain ID domain_idd1icfi_
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
Domain ID domain_idd1icfj_
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 (6 domains)

Domain ID domain_id1icfA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1icfB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily170 — Cysteine proteinases. Chain C
Domain ID domain_id1icfC00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1icfD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily170 — Cysteine proteinases. Chain C
Domain ID domain_id1icfI00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology800 — Invariant Chain; Chain I
Homologous superfamily homologous superfamily10 — Thyroglobulin type-1
Domain ID domain_id1icfJ00
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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7. Citations (1)