Research workbench
Crystal structure of anti-23F strep Fab C05 with rhamnose
Analyse Crystal structure of anti-23F strep Fab C05 with rhamnose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PTU
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody PN132P2C05, light chain; Antibody PN132P2C05, heavy chain
- Ligands
- RAM
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody PN132P2C05, light chain | protein | 212 | 6% helix, 50% strand | — |
| B | Antibody PN132P2C05, heavy chain | protein | 218 | 8% helix, 51% strand | — |
Ligands and binding sites
- RAM · alpha-L-rhamnopyranose · sugar · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.49 | 0.74 | 34 | ACT |
| 2 | 65 | 0.32 | 0.75 | 17 | RAM |
Interfaces
1 interface between chains.
- A–B · 1903 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4PTU · Crystal Structure of anti-23F strep Fab C05 with rhamnose · 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 4PTU · PDBe 4PTU
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