1ICF
CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L
- PDB DOI: https://doi.org/10.2210/pdb1ICF/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 1999-01-07 Released: 2000-01-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.182 
wwPDB Validation   3D Report Full Report
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PROTEIN (CATHEPSIN L: HEAVY CHAIN) | 175 | Homo sapiens | Mutation(s): 0  EC: 3.4.22.15 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711 | |||||
PHAROS:  P07711 GTEx:  ENSG00000135047  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07711 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PROTEIN (CATHEPSIN L: LIGHT CHAIN) | 42 | Homo sapiens | Mutation(s): 0  EC: 3.4.22.15 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711 | |||||
PHAROS:  P07711 GTEx:  ENSG00000135047  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07711 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PROTEIN (INVARIANT CHAIN) | E [auth I], F [auth J] | 65 | Homo sapiens | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233 | |||||
PHAROS:  P04233 GTEx:  ENSG00000019582  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04233 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth I], H [auth J] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.182 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 62.592 | α = 90 |
b = 80.594 | β = 96.77 |
c = 64.245 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
MAIN | refinement |
Entry History 
Deposition Data
- Released Date: 2000-01-12  Deposition Author(s): Guncar, G., Pungercic, G., Klemencic, I., Turk, V., Turk, D.
Revision History (Full details and data files)
- Version 1.0: 2000-01-12
Type: Initial release - Version 1.1: 2007-10-16
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.4: 2023-08-09
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary