MolNFT v1 · #107321 · protein

Mechanisms of neutralization of a human anti-alpha toxin antibody

4U6V · Fab, antigen binding fragment, heavy chain: “Mechanisms of neutralization of a human anti-alpha toxin antibody”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.61). MolNFT v1 #107321 on GenesisL1: 3D structure…

PDB: 4U6V
Type: protein
Length: 1,406 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab, antigen binding fragment, heavy chain; Fab, antigen binding fragment, light chain…
UniProt: Q2G1X0
Ligands: SO4
Pockets: 14 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, K	Fab, antigen binding fragment, heavy chain	protein	218	7% helix, 53% strand	—
L, M	Fab, antigen binding fragment, light chain	protein	213	6% helix, 50% strand	—
A, B	Alpha-hemolysin	protein	272	2% helix, 60% strand	Q2G1X0

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains H, L, A, K, M

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

Pockets

14 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	68	0.61	0.91	17	empty
2	65	0.60	0.91	18	empty
3	160	0.55	0.81	26	empty
4	142	0.54	0.81	27	empty
5	246	0.52	0.76	30	empty

Interfaces

6 interfaces between chains.

K–M · 1706 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1668 Å² buried · 13 hydrogen bonds · protein-protein
H–A · 455 Å² buried · 9 hydrogen bonds · protein-protein
K–B · 449 Å² buried · 8 hydrogen bonds · protein-protein
L–A · 331 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4U6V · Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody · the same entry in another collection · chain A against A, TM-score 1.00
Q2G1X0 · AlphaFold monomer V2.0 prediction for alpha-hemolysin (Q2G1X0) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q2G1X0
Elsewhere: RCSB PDB 4U6V · PDBe 4U6V · UniProt Q2G1X0

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