8IUI | pdb_00008iui

Crystal structure of silkworm fibroinase complexed with E-64

• PDB DOI: https://doi.org/10.2210/pdb8IUI/pdb

• Classification: HYDROLASE
• Organism(s): Bombyx mori
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-03-24 Released: 2024-04-03 
• Deposition Author(s): Guo, P.C., Wang, Z., Zhao, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Crystal structure of silkworm fibroinase complexed with E64 silworm

Guo, P.C., Wang, Z., Zhao, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.62 kDa 
• Atom Count: 3,621 
• Modeled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroinase	A, B	218	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for Q6T9Z7 (Bombyx mori) Explore Q6T9Z7  Go to UniProtKB:  Q6T9Z7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64 (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.240 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.18	α = 90
b = 64.69	β = 97.641
c = 92.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Guo, P.C., Wang, Z., Zhao, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970468
National Natural Science Foundation of China (NSFC)	China	32030103

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary