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Crystal structure of tcda-A1 bound to A26.8 vhh

Analyse Crystal structure of tcda-A1 bound to A26.8 vhh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NBZ
Type: protein
Length: 529 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tcda; A26.8 vhh
UniProt: I6YE93
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tcda	protein	136	0% helix, 51% strand	I6YE93
B	A26.8 vhh	protein	132	13% helix, 43% strand	—
C	Tcda	protein	138	0% helix, 49% strand	I6YE93
D	A26.8 vhh	protein	123	11% helix, 46% strand	—

Pockets

2 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	130	0.50	0.80	17	empty
2	90	0.34	0.74	17	empty

Interfaces

3 interfaces between chains.

A–B · 537 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 535 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 174 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4NBZ · Crystal Structure of TcdA-A1 Bound to A26.8 VHH · 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
Every structure of UniProt I6YE93
Elsewhere: RCSB PDB 4NBZ · PDBe 4NBZ · UniProt I6YE93

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