5MBM | pdb_00005mbm

Cathepsin B in complex with DARPin 8h6

• PDB DOI: https://doi.org/10.2210/pdb5MBM/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: 2.76 Å
• R-Value Free: 
  0.281 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: other

Literature

Cathepsin B in complex with DARPin 8h6

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.58 kDa 
• Atom Count: 6,499 
• Modeled Residue Count: 837 
• Deposited Residue Count: 854 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A, B	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 8h6	C, D	171	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.281 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.45	α = 90
b = 201.52	β = 90
c = 46.86	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	P1000048

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2024-05-01
  Changes: Advisory, Data collection, Database references, Refinement description