MolNFT v1 · #98848 · protein
Crystal structure of pertuzumab clambda Fab with variable domain redesign (VRD2) at 1.95A
4LLW · Mutated pertuzumab Fab heavy chain: “Crystal structure of pertuzumab clambda Fab with variable domain redesign (VRD2) at 1.95A”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.60). MolNFT v1 #98848 on GenesisL1…
- 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.