MolNFT v1 · #171755 · protein

Structure of alpha-cobratoxin with a peptide inhibitor

6ZFM: “Structure of alpha-cobratoxin with a peptide inhibitor”. X-ray diffraction, 1 ligand (QJE), 2 pockets (best druggability 0.72). MolNFT v1 #171755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZFM
Type: protein
Length: 288 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-cobratoxin; Peptide 12
UniProt: P01391
Ligands: QJE
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Alpha-cobratoxin	protein	71	6% helix, 38% strand	P01391
B, E	Alpha-cobratoxin	protein	65	6% helix, 35% strand	P01391
C, F	Peptide 12	protein	8	0% helix, 13% strand	—

Ligands and binding sites

QJE · 3-[2-[2-[2-[2-[2-(2-azanylethoxy) ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propan-1-ol · ligand · 2 copies · chains B, C, E, F
1PE · Pentaethylene glycol · additive · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.72	0.84	32	1PE
2	67	0.32	0.75	16	empty

Interfaces

14 interfaces between chains.

B–C · 507 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 502 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 454 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 454 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 440 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6ZFM · Structure of alpha-Cobratoxin with a peptide inhibitor · the same entry in another collection · chain F against F, TM-score 1.00
P01391 · AlphaFold monomer V2.0 prediction for alpha-cobratoxin (P01391) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P01391
Elsewhere: RCSB PDB 6ZFM · PDBe 6ZFM · UniProt P01391

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