Research workbench
Diabody 305 complex with epor
Analyse Diabody 305 complex with epor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y5X
- Type
- protein
- Length
- 1,762 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diabody 310 vl domain; Diabody 310 vh domain; Erythropoietin receptor
- UniProt
- Q5NV67, P19235
- Pockets
- 17 · best druggability 0.60
Structure
x-ray diffraction · 7 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Diabody 310 vl domain | protein | 124 | 5% helix, 50% strand | — |
| B, E, K | Diabody 310 vh domain | protein | 111 | 3% helix, 48% strand | Q5NV67 |
| C | Erythropoietin receptor | protein | 205 | 8% helix, 46% strand | P19235 |
| F | Erythropoietin receptor | protein | 206 | 9% helix, 47% strand | P19235 |
| H | Diabody 310 vh domain | protein | 109 | 3% helix, 49% strand | Q5NV67 |
| I | Erythropoietin receptor | protein | 207 | 8% helix, 44% strand | P19235 |
| L | Erythropoietin receptor | protein | 206 | 9% helix, 46% strand | P19235 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B, C, L, E, F, I, G, H, J, K
- FLC · Citrate anion · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.60 | 0.73 | 68 | empty |
| 2 | 389 | 0.59 | 0.76 | 65 | PEG |
| 3 | 303 | 0.56 | 0.76 | 48 | PEG |
| 4 | 313 | 0.56 | 0.76 | 47 | empty |
| 5 | 287 | 0.55 | 0.76 | 41 | PEG |
Interfaces
21 interfaces between chains.
- F–I · 1142 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 1108 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 926 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 7 hydrogen bonds · protein-protein
- J–K · 916 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4Y5X · Diabody 305 complex with EpoR · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q5NV67
- Every structure of UniProt P19235
- Elsewhere: RCSB PDB 4Y5X · PDBe 4Y5X · UniProt Q5NV67 · UniProt P19235
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