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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
- 3BD4
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalytic antibody
- Ligands
- CD
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalytic antibody | protein | 112 | 3% helix, 52% strand | — |
| B | Catalytic antibody | protein | 108 | 3% helix, 54% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.25 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 493 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BD4 · 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 3BD4 · PDBe 3BD4
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