7L33 | pdb_00007l33

X-ray Structure of a Cu-Bound De Novo Designed Peptide Trimer

PDB DOI: https://doi.org/10.2210/pdb7L33/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2020-12-17 Released: 2021-08-11
Deposition Author(s): Chakraborty, S., Wawrzak, Z., Prasad, P., Mitra, S., Prakash, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.294 (Depositor), 0.297 (DCC)
R-Value Work:
0.269 (Depositor), 0.273 (DCC)
R-Value Observed:
0.270 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7L33

This is version 1.2 of the entry. See complete history.

Literature

De Novo Design of a Self-Assembled Artificial Copper Peptide that Activates and Reduces Peroxide

Mitra, S., Prakash, D., Rajabimoghadam, K., Wawrzak, Z., Prasad, P., Wu, T., Misra, S.K., Sharp, J.S., Garcia-Bosch, I., Chakraborty, S.

(2021) ACS Catal 11: 10267-10278

DOI: https://doi.org/10.1021/acscatal.1c02132

Macromolecule Content

Total Structure Weight: 9.97 kDa
Atom Count: 702
Modeled Residue Count: 95
Deposited Residue Count: 96
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cu-3SCC	A, B, C	32	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.294 (Depositor), 0.297 (DCC)
R-Value Work: 0.269 (Depositor), 0.273 (DCC)
R-Value Observed: 0.270 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.26	α = 90
b = 39.26	β = 90
c = 83.63	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Chakraborty, S.

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
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.