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 
• Deposition Author(s): Guncar, G., Pungercic, G., Klemencic, I., Turk, V., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.72 kDa 
• Atom Count: 5,060 
• Modelled Residue Count: 564 
• Deposited Residue Count: 564 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATHEPSIN L: HEAVY CHAIN)	A, C	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATHEPSIN L: LIGHT CHAIN)	B, D	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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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 Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
MAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-12 
Deposition Author(s): Guncar, G., Pungercic, G., Klemencic, I., Turk, V., Turk, D.

Revision History  

• 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