ISDA: 9YZP

Deposition Date 2025-10-30

Release Date 2026-02-18

Last Version Date 2026-02-18

Entry Detail

PDB ID:

9YZP

Keywords:

DNA BINDING PROTEIN

Title:

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with ultrabithorax homeodomain

Biological Source:

Source Organism(s):

Drosophila melanogaster (Taxon ID: 7227)
Escherichia coli (Taxon ID: 562)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.67 Å

R-Value Free:

0.29

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

I 1 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:B (auth: A)
Chain Length:31
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:C (auth: B)
Chain Length:31
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Replication initiation protein
Gene (Uniprot):repE
Chain IDs:D (auth: C)
Chain Length:263
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P03856

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Homeotic protein ultrabithorax
Gene (Uniprot):Ubx
Chain IDs:A (auth: D)
Chain Length:62
Number of Molecules:1
Biological Source:Drosophila melanogaster

UniProt ID:P83949 Pfam ID:PF00046

Ligand Molecules

Primary Citation

Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins

Shields, E.T, Slaughter, C.K, Mekkaoui, F, Magna, E.N, Shepherd, C, Lukeman, P.S, Spratt, D.E, Snow, C.D, Liebschner, D, Afonine, P.V, Baker, M.L, Bunkoczi, G, Chen, V.B, Croll, T.I, Hintze, B, Hung, L.W, Jain, S, McCoy, A.J, Moriarty, N.W, Oeffner, R.D, Poon, B.K, Prisant, M.G, Read, R.J, Richardson, J.S, Richardson, D.C, Sammito, M.D, Sobolev, O.V, Stockwell, D.H, Terwilliger, T.C, Urzhumtsev, A.G, Videau, L.L, Williams, C.J, Adams, P.D.Show

To Be Published ? ? ? (?)

Primary Citation of related structures

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