Research workbench
Crystal structure of pertuzumab clambda Fab with variable domain redesign (VRD2) at 1.95A
Analyse Crystal structure of pertuzumab clambda Fab with variable domain redesign… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LLW
- Type
- protein
- Length
- 843 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
- SO4
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mutated pertuzumab Fab heavy chain | protein | 213 | 8% helix, 55% strand | — |
| B | Light chain clambda | protein | 207 | 7% helix, 51% strand | — |
| C | Mutated pertuzumab Fab heavy chain | protein | 214 | 10% helix, 54% strand | — |
| D | Light chain clambda | protein | 209 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.60 | 0.75 | 61 | SO4 |
| 2 | 103 | 0.40 | 0.77 | 22 | empty |
| 3 | 106 | 0.36 | 0.74 | 24 | empty |
| 4 | 74 | 0.35 | 0.76 | 21 | empty |
| 5 | 93 | 0.35 | 0.74 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1733 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1585 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4LLW · Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A · 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 4LLW · PDBe 4LLW
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.