8B45 | pdb_00008b45

Structure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4

PDB DOI: https://doi.org/10.2210/pdb8B45/pdb

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

Deposited: 2022-09-19 Released: 2023-09-27
Deposition Author(s): Kumar, P., Martin, F.J.O., Dawson, W.M., Zieleniewski, F., Woolfson, D.N.
Funding Organization(s): European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.214 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4

Kumar, P., Martin, F.J.O., Dawson, W.M., Zieleniewski, F., Woolfson, D.N.

To be published.

Macromolecule Content

Total Structure Weight: 13.88 kDa
Atom Count: 1,003
Modeled Residue Count: 122
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CC-Tri-(UbUc)4	A [auth B], B [auth C], C [auth D], D [auth A]	32	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] H [auth C] I [auth D] J [auth D] E [auth B], F [auth B], H [auth C], I [auth D], J [auth D], K [auth D], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	A [auth B], B [auth C], C [auth D], D [auth A]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.214 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.200 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.515	α = 90
b = 85.515	β = 90
c = 85.515	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Arcimboldo	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	340764
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L01386X/1
Engineering and Physical Sciences Research Council	United Kingdom	EP/G036764
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R00661X/1