Research workbench
Structure of a single-domain camelid antibody fragment cab-H7S specific of the blap beta-lactamase from bacillus licheniformis
Analyse Structure of a single-domain camelid antibody fragment cab-H7S specific of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M3J
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camelid heavy-chain antibody variable fragment cab-H7S
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camelid heavy-chain antibody variable fragment cab-H7S | protein | 116 | 8% helix, 59% strand | — |
| B | Camelid heavy-chain antibody variable fragment cab-H7S | protein | 119 | 5% helix, 57% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.57 | 0.88 | 15 | empty |
| 2 | 85 | 0.57 | 0.87 | 16 | empty |
| 3 | 64 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 388 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4M3J · Structure of a single-domain camelid antibody fragment cAb-H7S specific of the BlaP… · 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 4M3J · PDBe 4M3J
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