MolNFT v1 · #98850 · protein
Crystal structure of pertuzumab clambda Fab with variable and constant domain redesigns (VRD2 and CRD2) at 1.6A
4LLY · Mutated pertuzumab Fab heavy chain: “Crystal structure of pertuzumab clambda Fab with variable and constant domain redesigns (VRD2 and CRD2) at…”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.81). MolNFT v1…
- 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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