MolNFT v1 · #15668 · protein

An autoantibody to single-stranded DNA: comparison of the three- dimensional structures of the unliganded Fab and a deoxynucleotide- Fab complex

1NBV · IGG2B-kappa BV04-01 Fab (light chain): “An autoantibody to single-stranded DNA: comparison of the three- dimensional structures of the unliganded Fab…”. X-ray diffraction, 8 pockets (best druggability 0.43). MolNFT v1 #15668 on…

PDB: 1NBV
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG2B-kappa BV04-01 Fab (light chain); IGG2B-kappa BV04-01 Fab (heavy chain)
UniProt: P01867
Pockets: 8 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IGG2B-kappa BV04-01 Fab (light chain)	protein	219	5% helix, 48% strand	—
H	IGG2B-kappa BV04-01 Fab (heavy chain)	protein	219	4% helix, 49% strand	P01867

Pockets

8 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	92	0.43	0.79	25	empty
2	126	0.42	0.75	25	empty
3	124	0.37	0.73	23	empty
4	122	0.36	0.73	19	empty
5	93	0.36	0.75	23	empty

Interfaces

1 interface between chains.

L–H · 1903 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1NBV · An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of… · the same entry in another collection · chain L against L, TM-score 1.00
P01867 · AlphaFold monomer V2.0 prediction for ig gamma-2B chain C region (P01867) · a predicted model of the same protein · chain H against A, TM-score 0.47

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 P01867
Elsewhere: RCSB PDB 1NBV · PDBe 1NBV · UniProt P01867

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