Research workbench
Crystal structure of pertuzumab clambda Fab with variable and constant domain redesigns (VRD2 and CRD2) at 1.6A
Analyse Crystal structure of pertuzumab clambda Fab with variable and constant domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LLY
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutated pertuzumab Fab heavy chain; Light chain clambda
- Ligands
- MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mutated pertuzumab Fab heavy chain | protein | 220 | 11% helix, 54% strand | — |
| B, D | Light chain clambda | protein | 209 | 7% helix, 52% 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.81 | 0.87 | 93 | GOL |
| 2 | 272 | 0.66 | 0.82 | 27 | empty |
| 3 | 162 | 0.65 | 0.86 | 27 | empty |
| 4 | 97 | 0.59 | 0.87 | 25 | empty |
| 5 | 169 | 0.44 | 0.75 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1707 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1665 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 663 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4LLY · Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns… · 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 4LLY · PDBe 4LLY
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