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Cryo-EM structure of the tc toxin TCDA1 in its pore state

Analyse Cryo-EM structure of the tc toxin TCDA1 in its pore state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LKI
Type: protein
Length: 7,135 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCDA1
UniProt: Q9RN43
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 43% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	TCDA1	protein	1427	43% helix, 12% strand	Q9RN43

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	886	0.82	0.84	79	empty
2	807	0.81	0.84	64	empty
3	698	0.81	0.85	70	empty
4	573	0.81	0.87	60	empty
5	796	0.81	0.84	61	empty

Interfaces

5 interfaces between chains.

A–B · 7004 Å² buried · 88 hydrogen bonds · protein-protein
D–E · 7003 Å² buried · 88 hydrogen bonds · protein-protein
C–D · 7000 Å² buried · 88 hydrogen bonds · protein-protein
A–E · 6986 Å² buried · 89 hydrogen bonds · protein-protein
B–C · 6986 Å² buried · 88 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 isopeptide (isopeptide).

Compared structures

5LKI · Cryo-EM structure of the Tc toxin TcdA1 in its pore state · the same entry in another collection · chain B against B, 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
Every structure of UniProt Q9RN43
Elsewhere: RCSB PDB 5LKI · PDBe 5LKI · UniProt Q9RN43

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