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Cards toxin, nicked

Analyse Cards toxin, nicked in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TLV
Type: protein
Length: 3,471 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylating toxin cards
EC: 2.4.2.-
UniProt: P75409
Ligands: SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 15% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	ADP-ribosylating toxin cards (EC 2.4.2.-)	protein	582	15% helix, 36% strand	P75409
B	ADP-ribosylating toxin cards (EC 2.4.2.-)	protein	580	15% helix, 36% strand	P75409
C	ADP-ribosylating toxin cards (EC 2.4.2.-)	protein	577	15% helix, 37% strand	P75409
D	ADP-ribosylating toxin cards (EC 2.4.2.-)	protein	577	15% helix, 37% strand	P75409
F	ADP-ribosylating toxin cards (EC 2.4.2.-)	protein	573	15% helix, 37% strand	P75409

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, C, D
GOL · Glycerol · additive · 27 copies · chains A, B, C, D, E, F
ACT · Acetate ion · additive · 4 copies · chains A, D, E

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

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	628	0.85	0.89	68	GOL
2	599	0.84	0.89	87	GOL
3	522	0.83	0.89	72	GOL
4	1042	0.82	0.83	108	SO4
5	275	0.77	0.90	54	empty

Interfaces

6 interfaces between chains.

E–F · 1670 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1622 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1601 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 727 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 705 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4TLV · Cards toxin, nicked · the same entry in another collection · chain F against F, TM-score 1.00
P75409 · AlphaFold monomer V2.0 prediction for ADP-ribosylating toxin cards (P75409) · a predicted model of the same protein · chain E 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 P75409
Elsewhere: RCSB PDB 4TLV · PDBe 4TLV · UniProt P75409

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