6TYD: Human LDB1

Structure of human LDB1 in complex with SSBP2. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,079
Mol. weight: 49.71 kDa
Released: 1 Jan 2020

Explore 6TYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TYD contains 19 α-helices and 9 β-strands across 3 chains. 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 A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	36-45	10
α-helix	51-52	2
α-helix	60-72	13
β-strand	80	1	2
β-strand	82	1	2
α-helix	87-93	7

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	15-33	19
α-helix	36-46	11
α-helix	56	1
α-helix	60-74	15

Chain V: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	68-78	11
α-helix	87-97	11
β-strand	98-108	11	1
β-strand	115-119	5	1
α-helix	121-123	3
α-helix	124-133	10
β-strand	136-144	9	1
α-helix	146	1
β-strand	147-150	4	1
β-strand	154-168	15	1
β-strand	175-187	13	1
β-strand	194-207	14	1
α-helix	210-215	6
α-helix	220-223	4
α-helix	224-227	4
α-helix	237-261	25
α-helix	266-281	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain-binding protein 1	V	protein	231	Homo sapiens	Q86U70 (AlphaFold model)
Single-stranded DNA-binding protein 2	A, B	protein	95	Homo sapiens	P81877 (AlphaFold model)

Sequence of entity 1 (V), FASTA

>6TYD_1 LIM domain-binding protein 1 (chains V)
GGIGRHTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGP
KRYTIGRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFT
QVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCG
LSNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPP

Sequence of entity 2 (A, B), FASTA

>6TYD_2 Single-stranded DNA-binding protein 2 (chains A, B)
GMYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPG
FLHSWWCVFWDLYCAAPERRETCEHSSEAKAFHDY

Primary citation

Crystal structure of human LDB1 in complex with SSBP2. Wang, H., Kim, J., Wang, Z. et al. Proc Natl Acad Sci U S A (2020) 117:1042-1048. DOI 10.1073/pnas.1914181117 · PubMed

Other PDB entries of the same protein (UniProt Q86U70 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OB5 1.8 Å, Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide
7OB8 1.8 Å, Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide and stabilizer…
9F5B 1.8 Å, Identification of zinc ions in LMO4.
2XJY 2.4 Å, Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form
8HIB 2.45 Å, The crystal structure of Pygo2-LDB1-SSBP2 triple complex
2XJZ 2.8 Å, Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form
2YPA 2.8 Å, Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA
8SSU 2.89 Å, ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA

Browse structure collections

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