Research workbench

Transmembrane protein 24 smp domain

Analyse Transmembrane protein 24 smp domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TOD
Type: protein
Length: 907 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transmembrane protein 24
UniProt: O14523
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 23% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Transmembrane protein 24	protein	150	25% helix, 53% strand	O14523
A, B	Transmembrane protein 24	protein	152	24% helix, 53% strand	O14523
C	Transmembrane protein 24	protein	144	22% helix, 56% strand	O14523
D	Transmembrane protein 24	protein	157	22% helix, 54% strand	O14523
E	Transmembrane protein 24	protein	152	22% helix, 53% strand	O14523

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	303	0.83	0.93	36	empty
2	366	0.82	0.91	49	empty
3	831	0.82	0.84	87	empty
4	698	0.82	0.85	62	empty
5	412	0.81	0.89	44	empty

Interfaces

9 interfaces between chains.

A–D · 836 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 833 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 816 Å² buried · 12 hydrogen bonds · protein-protein
F–C · 692 Å² buried · 12 hydrogen bonds · protein-protein
F–E · 654 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

5TOD · Transmembrane protein 24 SMP domain · the same entry in another collection · chain E against E, TM-score 1.00
O14523 · AlphaFold monomer V2.0 prediction for phospholipid transfer protein C2CD2L (O14523) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 O14523
Elsewhere: RCSB PDB 5TOD · PDBe 5TOD · UniProt O14523

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