Research workbench

DENOVOTIM6-sb, a de novo designed tim barrel with a salt-bridge cluster (crystal form 2)

Analyse DENOVOTIM6-sb, a de novo designed tim barrel with a salt-bridge cluster… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OT8
Type: protein
Length: 346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DENOVOTIM6-sb
Ligands: SO4
Pockets: 4 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DENOVOTIM6-sb	protein	172	46% helix, 22% strand	—
B	DENOVOTIM6-sb	protein	174	41% helix, 22% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.39	0.77	20	empty
2	60	0.37	0.79	19	empty
3	102	0.35	0.74	21	empty
4	55	0.33	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 332 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7OT8 · DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 2) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7OT8 · PDBe 7OT8

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