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Crystal structure of single domain vl of an anti-DNA binding antibody 3D8 scfv and its active site revealed by complex structures of a small molecule and metals

Analyse Crystal structure of single domain vl of an anti-DNA binding antibody 3D8 scfv… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BD3
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic antibody
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Catalytic antibody	protein	112	3% helix, 51% strand	—

Ligands and binding sites

BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.29	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 621 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3BD3 · Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its… · the same entry in another collection · chain A against A, 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 3BD3 · PDBe 3BD3

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