MolNFT v1 · #98846 · protein
Structure of pertuzumab Fab with light chain clambda at 2.16A
4LLU · Pertuzumab Fab heavy chain: “Structure of pertuzumab Fab with light chain clambda at 2.16A”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.80). MolNFT v1 #98846 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LLU
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertuzumab Fab heavy chain; Light chain clambda
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pertuzumab Fab heavy chain | protein | 220 | 7% helix, 54% strand | — |
| B | Light chain clambda | protein | 210 | 6% helix, 51% strand | — |
| D | Light chain clambda | protein | 206 | 5% helix, 49% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.80 | 0.82 | 90 | empty |
| 2 | 634 | 0.69 | 0.78 | 54 | empty |
| 3 | 403 | 0.64 | 0.78 | 46 | empty |
| 4 | 123 | 0.48 | 0.79 | 29 | empty |
| 5 | 133 | 0.42 | 0.75 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1932 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1790 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 165 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4LLU · Structure of Pertuzumab Fab with light chain Clambda at 2.16A · 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 4LLU · PDBe 4LLU
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