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Crystal structure of inhibitory smad, SMAD7

Analyse Crystal structure of inhibitory smad, SMAD7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CD1
Type: protein
Length: 720 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mothers against decapentaplegic homolog 7
UniProt: O35253
Ligands: SO4, CL
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mothers against decapentaplegic homolog 7	protein	180	17% helix, 34% strand	O35253

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
CL · Chloride ion · ion · 7 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	446	0.74	0.84	56	empty
2	433	0.72	0.82	49	empty
3	65	0.65	0.93	17	empty
4	204	0.60	0.81	27	empty
5	152	0.53	0.80	28	empty

Interfaces

5 interfaces between chains.

A–C · 2168 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 2096 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 868 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 458 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 381 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7CD1 · Crystal structure of inhibitory Smad, Smad7 · the same entry in another collection · chain A against A, TM-score 1.00
O35253 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 7 (O35253) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 O35253
Elsewhere: RCSB PDB 7CD1 · PDBe 7CD1 · UniProt O35253

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