MolNFT v1 · #127826 · protein

Crystal structure of antibody bound to viral protein

5N88 · VH59 antibody: “Crystal structure of antibody bound to viral protein”. X-ray diffraction, 3 pockets (best druggability 0.43). MolNFT v1 #127826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5N88
Type: protein
Length: 411 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VH59 antibody; PC4 and SFRS1-interacting protein
UniProt: O75475
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	VH59 antibody	protein	126	10% helix, 49% strand	—
D	PC4 and SFRS1-interacting protein	protein	79	75% helix, 1% strand	O75475
E	PC4 and SFRS1-interacting protein	protein	80	74% helix, 1% strand	O75475

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.43	0.76	24	empty
2	184	0.43	0.73	35	empty
3	95	0.39	0.77	24	empty

Interfaces

4 interfaces between chains.

H–E · 712 Å² buried · 5 hydrogen bonds · protein-protein
D–A · 677 Å² buried · 5 hydrogen bonds · protein-protein
H–D · 345 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 19 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5N88 · Crystal structure of antibody bound to viral protein · the same entry in another collection · chain H against H, TM-score 1.00
O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 O75475
Elsewhere: RCSB PDB 5N88 · PDBe 5N88 · UniProt O75475

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