Research workbench
Crystal structure of extracellular domain of human ERBB4/HER4 in complex with the Fab fragment of MAB1479
Analyse Crystal structure of extracellular domain of human ERBB4/HER4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U9U
- Type
- protein
- Length
- 2,037 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Receptor tyrosine-protein kinase erbb-4
- EC
- 2.7.10.1
- UniProt
- Q15303
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 219 | 4% helix, 51% strand | — |
| B, D | Fab light chain | protein | 219 | 6% helix, 50% strand | — |
| C | Fab heavy chain | protein | 215 | 4% helix, 50% strand | — |
| E | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.10.1) | protein | 585 | 9% helix, 26% strand | Q15303 |
| F | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.10.1) | protein | 580 | 10% helix, 25% strand | Q15303 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.70 | 0.78 | 66 | empty |
| 2 | 462 | 0.65 | 0.78 | 57 | empty |
| 3 | 562 | 0.62 | 0.74 | 50 | empty |
| 4 | 140 | 0.55 | 0.82 | 21 | empty |
| 5 | 276 | 0.53 | 0.75 | 34 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2098 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1989 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 501 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 498 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 466 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide (disulfide).
Compared structures
- 3U9U · Crystal Structure of Extracellular Domain of Human ErbB4/Her4 in complex with the Fab… · the same entry in another collection · chain D against D, TM-score 1.00
- Q15303 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-4 (Q15303) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 Q15303
- Elsewhere: RCSB PDB 3U9U · PDBe 3U9U · UniProt Q15303
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