8UQF | pdb_00008uqf

Crystal structure of designed cortisol-binding protein hcy129_mpnn5

PDB DOI: https://doi.org/10.2210/pdb8UQF/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-23 Released: 2024-11-20
Deposition Author(s): Pellock, S.J., Bera, A.
Funding Organization(s): Other private, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Small molecule binding and sensing with a designed protein family

Lee, G.R., Pellock, S.J., Norn, C., Tischer, D., Dauparas, J., Anischenko, I., Mercer, J.A.M., Kang, A., Bera, A., Nguyen, H., Goreshnik, I., Vafeados, D., Roullier, N., Han, H.L., Coventry, B., Liu, D.R., Yeh, A.H.W.

To be published.

Macromolecule Content

Total Structure Weight: 31.63 kDa
Atom Count: 2,155
Modeled Residue Count: 246
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed cortisol-binding protein hcy129_mpnn5	A, B	135	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HCY (Subject of Investigation/LOI) Query on HCY 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]	(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione C₂₁ H₃₀ O₅ JYGXADMDTFJGBT-VWUMJDOOSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.016	α = 90
b = 48.609	β = 93.99
c = 56.438	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

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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.