MolNFT v1 · #188137 · protein

Cryoem structure of sfab cop-2 complex with human claudin-4 and clostridium perfringens enterotoxin C-terminal domain

7TDM: “Cryoem structure of sfab cop-2 complex with human claudin-4 and clostridium perfringens enterotoxin…”. Electron microscopy, 14 pockets (best druggability 0.87). MolNFT v1 #188137 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7TDM
Type: protein
Length: 750 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Claudin-4; Heat-labile enterotoxin B chain; Cop-2 Fab heavy chain; Cop-2 Fab light chain
UniProt: O14493, P01558
Pockets: 14 · best druggability 0.87

Structure

electron microscopy · 4 distinct chains · 17% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Claudin-4	protein	182	55% helix, 9% strand	O14493
B	Heat-labile enterotoxin B chain	protein	128	5% helix, 44% strand	P01558
H	Cop-2 Fab heavy chain	protein	226	3% helix, 41% strand	—
L	Cop-2 Fab light chain	protein	214	7% helix, 38% strand	—

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.87	0.88	107	empty
2	117	0.76	0.95	32	empty
3	190	0.76	0.91	28	empty
4	81	0.73	0.96	21	empty
5	167	0.70	0.88	31	empty

Interfaces

4 interfaces between chains.

H–L · 1626 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 952 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 884 Å² buried · 7 hydrogen bonds · protein-protein
B–L · 269 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7TDM · CryoEM Structure of sFab COP-2 Complex with human claudin-4 and Clostridium perfringens… · the same entry in another collection · chain A against A, TM-score 1.00
O14493 · AlphaFold monomer V2.0 prediction for claudin-4 (O14493) · a predicted model of the same protein · chain A against A, TM-score 0.87
P01558 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P01558) · a predicted model of the same protein · chain B against A, TM-score 0.86

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 O14493
Every structure of UniProt P01558
Elsewhere: RCSB PDB 7TDM · PDBe 7TDM · UniProt O14493 · UniProt P01558

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