MolNFT v1 · #110748 · protein
Diabody 330 complex with epor
4Y5Y · Diabody 330 vh domain: “Diabody 330 complex with epor”. X-ray diffraction, 5 pockets (best druggability 0.58). MolNFT v1 #110748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y5Y
- Type
- protein
- Length
- 868 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diabody 330 vh domain; Diabody 330 vl domain; Erythropoietin receptor
- UniProt
- P19235
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diabody 330 vh domain | protein | 118 | 8% helix, 51% strand | — |
| B, E | Diabody 330 vl domain | protein | 112 | 5% helix, 46% strand | — |
| C | Erythropoietin receptor | protein | 198 | 10% helix, 48% strand | P19235 |
| D | Diabody 330 vh domain | protein | 119 | 10% helix, 50% strand | — |
| F | Erythropoietin receptor | protein | 209 | 10% helix, 45% strand | P19235 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.58 | 0.74 | 65 | empty |
| 2 | 82 | 0.42 | 0.80 | 21 | empty |
| 3 | 74 | 0.41 | 0.80 | 22 | empty |
| 4 | 109 | 0.36 | 0.74 | 16 | empty |
| 5 | 94 | 0.35 | 0.74 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 953 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 926 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 591 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 571 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 8 disulfide (methylation, disulfide).
Compared structures
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 P19235
- Elsewhere: RCSB PDB 4Y5Y · PDBe 4Y5Y · UniProt P19235
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