MolNFT v1 · #52342 · protein

Crystal structure of murine reference antibody 125-2H Fab fragment

2VXU · Murine IgG 125-2H: “Crystal structure of murine reference antibody 125-2H Fab fragment”. X-ray diffraction, 9 pockets (best druggability 0.68). MolNFT v1 #52342 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VXU
Type: protein
Length: 860 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Murine IgG 125-2H
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, I	Murine IgG 125-2H	protein	216	6% helix, 51% strand	—
L, M	Murine IgG 125-2H	protein	214	6% helix, 51% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	711	0.68	0.76	87	empty
2	170	0.53	0.79	28	empty
3	230	0.46	0.73	25	empty
4	213	0.46	0.73	38	empty
5	166	0.42	0.74	30	empty

Interfaces

6 interfaces between chains.

H–L · 1816 Å² buried · 17 hydrogen bonds · protein-protein
I–M · 1751 Å² buried · 17 hydrogen bonds · protein-protein
I–L · 232 Å² buried · 2 hydrogen bonds · protein-protein
H–I · 114 Å² buried · 1 hydrogen bond · protein-protein
L–M · 64 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

2VXU · Crystal structure of murine reference antibody 125-2H Fab fragment · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 2VXU · PDBe 2VXU

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.