5BQD: TBX5 (1-239) Dimer

Name: PDB 5BQD: Crystal Structure of TBX5 (1-239) Dimer
Published: 2016-03-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal Structure of TBX5 (1-239) Dimer. Determined by X-ray diffraction at 2.58 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,039
Mol. weight: 53.67 kDa
Ligands: MG
Released: 16 Mar 2016

Explore 5BQD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BQD contains 13 α-helices and 33 β-strands across 2 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: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
β-strand	43-48	6	1
β-strand	55-58	4	2
α-helix	61-70	10
β-strand	73-75	3	1
β-strand	77	1	3
β-strand	81-82	2	3
β-strand	88-92	5	2
β-strand	99-108	10	1
β-strand	113-117	5	4
β-strand	120-125	6	4
α-helix	131-134	4
β-strand	136-137	2	1
β-strand	143-144	2	1
α-helix	145-150	6
β-strand	153-154	2	2
β-strand	159-161	3	3
α-helix	170	1
β-strand	171-172	2	3
β-strand	178-187	10	1
β-strand	200-205	6	1
α-helix	207-209	3
β-strand	211-214	4	1
α-helix	220-227	8

Chain B: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	5
α-helix	61-70	10
β-strand	73-75	3	1
β-strand	77	1	6
β-strand	81-82	2	6
α-helix	83	1
β-strand	88-92	5	5
β-strand	99-108	10	1
β-strand	112-117	6	7
β-strand	120-126	7	7
β-strand	136-137	2	1
β-strand	143-144	2	1
α-helix	145-150	6
β-strand	153-154	2	5
β-strand	159-161	3	6
α-helix	170	1
β-strand	171-172	2	6
β-strand	178-187	10	1
β-strand	200-205	6	1
α-helix	207-209	3
β-strand	211-214	4	1
α-helix	220-223	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-box transcription factor TBX5	A, B	protein	239	Homo sapiens	Q99593 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5BQD_1 T-box transcription factor TBX5 (chains A, B)
MADADEGFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFTQQGMEGIKVFLHE
RELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNK
WSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQ
PRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5. Pradhan, L., Gopal, S., Li, S. et al. Biochemistry (2016) 55:1702-1710. DOI 10.1021/acs.biochem.6b00171 · PubMed

Other PDB entries of the same protein (UniProt Q99593 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X6U 1.9 Å, Crystal structure of human TBX5 in the DNA-free form
2X6V 2.2 Å, Crystal structure of human TBX5 in the DNA-bound and DNA-free form
4S0H 2.82 Å, TBX5 DB, NKX2.5 HD, ANF DNA Complex

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