5MBL | pdb_00005mbl

Cathepsin B in complex with DARPin 81

• PDB DOI: https://doi.org/10.2210/pdb5MBL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-08 Released: 2017-12-20 
• Deposition Author(s): Turk, D., Kramer, L., Renko, M., Turk, B.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.193 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: other

Literature

Cathepsin B in complex with DARPin 81

Turk, D., Kramer, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 46.1 kDa 
• Atom Count: 3,779 
• Modeled Residue Count: 420 
• Deposited Residue Count: 427 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A	256	Homo sapiens	Mutation(s): 0  Gene Names: CTSB, CPSB EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858  Go to UniProtKB:  P07858
PHAROS:  P07858 GTEx:  ENSG00000164733

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin 81	B	171	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.193 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.79	α = 90
b = 105.79	β = 90
c = 92.61	γ = 90

Software Package:

Software Name	Purpose
MAIN	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Turk, D., Kramer, L., Renko, M., Turk, B.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P100048

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Advisory, Data collection, Database references, Refinement description