Research workbench
DARPIN_D5/HER3 domain 4 complex, monoclinic crystals
Analyse DARPIN_D5/HER3 domain 4 complex, monoclinic crystals in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BHE
- Type
- protein
- Length
- 514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DARPIN_D5; Receptor tyrosine-protein kinase erbb-3
- EC
- 2.7.10.1
- UniProt
- P21860
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DARPIN_D5 | protein | 126 | 56% helix, 0% strand | — |
| B, D | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 131 | 2% helix, 35% strand | P21860 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.56 | 0.77 | 29 | empty |
| 2 | 136 | 0.56 | 0.82 | 32 | empty |
| 3 | 144 | 0.56 | 0.82 | 33 | empty |
| 4 | 250 | 0.55 | 0.77 | 31 | empty |
| 5 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 857 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 848 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 192 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 185 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 7BHE · DARPin_D5/Her3 domain 4 complex, monoclinic crystals · 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 D against A, TM-score 0.97
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 7BHE · PDBe 7BHE · UniProt P21860
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