8W6E

De novo design of HBC599 binder

PDB DOI: https://doi.org/10.2210/pdb8W6E/pdb

Classification: DE NOVO PROTEIN
Organism(s): artificial sequences
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-28 Released: 2024-11-27
Deposition Author(s): Liang, M.F., Zhu, J.Y., Lu, P.L.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.244
R-Value Work: 0.218
R-Value Observed: 0.219

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

De novo design of HBC599 binder

Liang, M.F., Zhu, J.Y., Lu, P.L.

To be published.

Macromolecule Content

Total Structure Weight: 43.64 kDa
Atom Count: 2,838
Modelled Residue Count: 320
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HBC599 in complex with wFAP1.1	A, B	170	artificial sequences	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KY6 (Subject of Investigation/LOI) Query on KY6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile C₂₁ H₁₇ N₃ O S WXTHEUULEXARCU-WOJGMQOQSA-N		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: 2.10 Å
R-Value Free: 0.244
R-Value Work: 0.218
R-Value Observed: 0.219
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.557	α = 90
b = 91.912	β = 107.791
c = 52.198	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0909200

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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.