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Crystal structure of TBX5 (1-239) dimer

Analyse Crystal structure of TBX5 (1-239) dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BQD
Type: protein
Length: 373 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-box transcription factor TBX5
UniProt: Q99593
Ligands: MG
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-box transcription factor TBX5	protein	197	14% helix, 37% strand	Q99593
B	T-box transcription factor TBX5	protein	176	13% helix, 39% strand	Q99593

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.74	0.81	61	empty
2	311	0.57	0.77	36	empty
3	70	0.41	0.80	23	empty
4	100	0.38	0.76	18	empty
5	71	0.31	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1029 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

Q99593 · AlphaFold monomer V2.0 prediction for T-box transcription factor TBX5 (Q99593) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q99593
Elsewhere: RCSB PDB 5BQD · PDBe 5BQD · UniProt Q99593

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