MolNFT v1 · #110745 · protein
Diabody 305 complex with epor
4Y5V · Diabody 305 vh domain: “Diabody 305 complex with epor”. X-ray diffraction, 18 pockets (best druggability 0.78). MolNFT v1 #110745 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y5V
- Type
- protein
- Length
- 1,300 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diabody 305 vh domain; Diabody 305 vl domain; Erythropoietin receptor
- UniProt
- P19235
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diabody 305 vh domain | protein | 121 | 10% helix, 50% strand | — |
| B | Diabody 305 vl domain | protein | 111 | 3% helix, 47% strand | — |
| C | Erythropoietin receptor | protein | 206 | 10% helix, 45% strand | P19235 |
| D | Diabody 305 vh domain | protein | 122 | 10% helix, 50% strand | — |
| E, H | Diabody 305 vl domain | protein | 112 | 3% helix, 46% strand | — |
| F | Erythropoietin receptor | protein | 206 | 10% helix, 45% strand | P19235 |
| G | Diabody 305 vh domain | protein | 119 | 10% helix, 51% strand | — |
| I | Erythropoietin receptor | protein | 191 | 9% helix, 46% strand | P19235 |
Ligands and binding sites
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D, E, F, G, H
- PGE · Triethylene glycol · additive · chains D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.78 | 0.80 | 92 | GOL |
| 2 | 117 | 0.59 | 0.85 | 23 | empty |
| 3 | 85 | 0.56 | 0.86 | 19 | empty |
| 4 | 85 | 0.50 | 0.83 | 23 | empty |
| 5 | 220 | 0.48 | 0.75 | 27 | GOL |
Interfaces
17 interfaces between chains.
- D–E · 870 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 857 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 849 Ų buried · 8 hydrogen bonds · protein-protein
- G–I · 585 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (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 4Y5V · PDBe 4Y5V · UniProt P19235
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