Research workbench
CH1/CLAMBDA Fab based on pertuzumab
Analyse CH1/CLAMBDA Fab based on pertuzumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VSH
- Type
- protein
- Length
- 1,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH1/CLAMBDA Fab heavy chain; CH1/CLAMBDA Fab light chain
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | CH1/CLAMBDA Fab heavy chain | protein | 214 | 7% helix, 56% strand | — |
| B, L | CH1/CLAMBDA Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| D, F | CH1/CLAMBDA Fab light chain | protein | 211 | 6% helix, 52% strand | — |
| E | CH1/CLAMBDA Fab heavy chain | protein | 212 | 7% helix, 55% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.63 | 0.74 | 57 | SO4 |
| 2 | 558 | 0.60 | 0.73 | 58 | SO4 |
| 3 | 531 | 0.60 | 0.74 | 54 | empty |
| 4 | 551 | 0.60 | 0.73 | 62 | SO4 |
| 5 | 551 | 0.59 | 0.73 | 63 | SO4 |
Interfaces
11 interfaces between chains.
- H–L · 1889 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1868 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1779 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1726 Ų buried · 13 hydrogen bonds · protein-protein
- C–L · 300 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5VSH · CH1/Clambda Fab based on Pertuzumab · 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 5VSH · PDBe 5VSH
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