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)

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), 0.233 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of silkworm fibroinase complexed with E64 silworm

Guo, P.C., Wang, Z., Zhao, P.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6T9Z7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E64 (Subject of Investigation/LOI) Query on E64 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C₁₅ H₃₀ N₅ O₅ QPQNJAXBPHVASB-QWRGUYRKSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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), 0.233 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.