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Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular domains of human HER3 (ERBB3)
Analyse Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LEO
- Type
- protein
- Length
- 1,034 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RG7116 Fab heavy chain; RG7116 Fab light chain; Receptor tyrosine-protein kinase erbb-3
- EC
- 2.7.10.1
- UniProt
- P21860
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RG7116 Fab heavy chain | protein | 214 | 6% helix, 55% strand | — |
| B | RG7116 Fab light chain | protein | 219 | 6% helix, 50% strand | — |
| C | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 601 | 9% helix, 28% strand | P21860 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.61 | 0.75 | 62 | empty |
| 2 | 182 | 0.47 | 0.75 | 30 | empty |
| 3 | 110 | 0.43 | 0.78 | 28 | NAG |
| 4 | 54 | 0.42 | 0.83 | 16 | empty |
| 5 | 117 | 0.40 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1840 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 672 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 401 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4LEO · Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular domains of… · the same entry in another collection · chain A against A, TM-score 1.00
- P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain C against A, TM-score 0.84
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21860
- Elsewhere: RCSB PDB 4LEO · PDBe 4LEO · UniProt P21860
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