5U5C | pdb_00005u5c

Coiled Coil Peptide Metal Coordination Framework: Tetramer Fold

PDB DOI: https://doi.org/10.2210/pdb5U5C/pdb

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

Deposited: 2016-12-06 Released: 2017-02-22
Deposition Author(s): Tavenor, N.A., Murnin, M.J., Horne, W.S.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.276 (Depositor), 0.281 (DCC)
R-Value Work:
0.263 (Depositor), 0.265 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Supramolecular Metal-Coordination Polymers, Nets, and Frameworks from Synthetic Coiled-Coil Peptides.

Tavenor, N.A., Murnin, M.J., Horne, W.S.

(2017) J Am Chem Soc 139: 2212-2215

PubMed: 28161945 Search on PubMed
DOI: https://doi.org/10.1021/jacs.7b00651
Primary Citation of Related Structures:
5U59, 5U5A, 5U5B, 5U5C

PubMed Abstract:
Metal coordination and peptide-directed self-assembly are two proven methods for creating defined supramolecular architectures. Here, we report a new class of crystalline materials based on coiled-coil peptides bearing unnatural metal-chelating terpyridine moieties. High-resolution structural characterization of lattices formed in the presence of Cu ²⁺ reveals a general assembly mechanism. Subtle sequence variation in the modular synthetic ligand dictates assembly morphology.

Organizational Affiliation

Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.

Macromolecule Content

Total Structure Weight: 20.38 kDa
Atom Count: 1,579
Modeled Residue Count: 180
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed tetrameric coiled coil peptide with one terpyridine side chain	A, B, C, D, E A, B, C, D, E, F	30	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain I [auth C] MOL2 format, chain N [auth E] MOL2 format, chain I [auth C] mmCIF format, chain N [auth E] mmCIF format, chain I [auth C]	I [auth C], N [auth E]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain N [auth E] Interactions & Density Focus chain I [auth C] Focus chain N [auth E]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain M [auth E] SDF format, chain L [auth E] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain M [auth E] MOL2 format, chain L [auth E] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain M [auth E] mmCIF format, chain L [auth E]	G [auth B] H [auth C] J [auth D] K [auth E] L [auth E] G [auth B], H [auth C], J [auth D], K [auth E], L [auth E], M [auth E]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.276 (Depositor), 0.281 (DCC)
R-Value Work: 0.263 (Depositor), 0.265 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.297	α = 90
b = 38.642	β = 90
c = 44.198	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Tavenor, N.A.

Murnin, M.J.

Horne, W.S.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR1149067

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection, Derived calculations
Version 1.5: 2024-11-20
Changes: Structure summary