1UBD: Protein

Co-crystal structure of human YY1 zinc finger domain bound to the adeno-associated virus P5 initiator element. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 Dec 1996.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,809
Mol. weight: 26.72 kDa
Ligands: ZN
Released: 23 Dec 1996

Explore 1UBD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1UBD contains 7 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	296-297	2	1
α-helix	298	1
β-strand	306-307	2	1
α-helix	310-317	8
α-helix	318-320	3
β-strand	325-326	2	2
β-strand	333-334	2	2
α-helix	337-343	7
α-helix	344-346	3
β-strand	353-354	2	3
β-strand	363-364	2	3
α-helix	367-378	12
α-helix	401-407	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(apgpgpgptpcptpcpcpaptptptptpgpapa pgpcpg)-3')	A	DNA	20
DNA (5'-d(cpgpcptptpcpapapapaptpgpgpapgpapc pcpcpt)-3')	B	DNA	20
Protein (YY1 zinc finger domain)	C	protein	124	Homo sapiens	P25490 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1UBD_1 DNA (5'-D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3') (chains A)
AGGGTCTCCATTTTGAAGCG

Sequence of entity 2 (B), FASTA

>1UBD_2 DNA (5'-D(*CP*GP*CP*TP*TP*CP*AP*AP*AP*AP*TP*GP*GP*AP*GP*AP*C P*CP*CP*T)-3') (chains B)
CGCTTCAAAATGGAGACCCT

Sequence of entity 3 (C), FASTA

>1UBD_3 PROTEIN (YY1 ZINC FINGER DOMAIN) (chains C)
MEPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGE
KPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKA
KNNQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Houbaviy, H.B., Usheva, A., Shenk, T. et al. Proc Natl Acad Sci U S A (1996) 93:13577-13582. DOI 10.1073/pnas.93.24.13577 · PubMed

Other PDB entries of the same protein (UniProt P25490 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C5I 2.59 Å, Crystal structure of MBTD1 YY1 complex
1ZNM A zinc finger with an artificial beta-turn, original sequence taken from the third zinc…

Browse structure collections

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