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Crystal structure of mouse claudin-3 P134A mutant in complex with C- terminal fragment of clostridium perfringens enterotoxin

Analyse Crystal structure of mouse claudin-3 P134A mutant in complex with C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AKF
Type: protein
Length: 1,181 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Claudin-3; Heat-labile enterotoxin B chain
UniProt: Q9Z0G9, P01558
Pockets: 16 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Claudin-3	protein	184	64% helix, 9% strand	Q9Z0G9
C	Claudin-3	protein	186	60% helix, 13% strand	Q9Z0G9
E	Claudin-3	protein	174	57% helix, 6% strand	Q9Z0G9
G	Claudin-3	protein	169	57% helix, 12% strand	Q9Z0G9
B, D, F, H	Heat-labile enterotoxin B chain	protein	117	7% helix, 43% strand	P01558

Pockets

16 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	391	0.68	0.81	56	empty
2	522	0.68	0.78	61	empty
3	407	0.67	0.80	46	empty
4	435	0.66	0.79	51	empty
5	311	0.58	0.77	40	empty

Interfaces

8 interfaces between chains.

C–D · 1212 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1167 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1097 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1066 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1059 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6AKF · Crystal structure of mouse claudin-3 P134A mutant in complex with C-terminal fragment of… · the same entry in another collection · chain H against H, TM-score 1.00
P01558 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P01558) · a predicted model of the same protein · chain D 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 Q9Z0G9
Every structure of UniProt P01558
Elsewhere: RCSB PDB 6AKF · PDBe 6AKF · UniProt Q9Z0G9 · UniProt P01558

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