MolNFT v1 · #111389 · protein
Structural insights into the neutralization properties of a human anti-interferon monoclonal antibody
4YPG · Sifalimumab light chain: “Structural insights into the neutralization properties of a human anti-interferon monoclonal antibody”. X-ray diffraction, 1 ligand (NI), 15 pockets (best druggability 0.56). MolNFT v1 #111389 on GenesisL1…
- PDB
- 4YPG
- Type
- protein
- Length
- 1,188 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sifalimumab light chain; Sifalimumab heavy chain; Interferon alpha-2
- UniProt
- Q6PJF2, P01563
- Ligands
- NI
- Pockets
- 15 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Sifalimumab light chain | protein | 215 | 8% helix, 47% strand | Q6PJF2 |
| B, H | Sifalimumab heavy chain | protein | 219 | 10% helix, 49% strand | — |
| C | Interferon alpha-2 | protein | 159 | 60% helix, 1% strand | P01563 |
| D | Interferon alpha-2 | protein | 161 | 64% helix, 0% strand | P01563 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.56 | 0.88 | 23 | empty |
| 2 | 356 | 0.55 | 0.75 | 44 | empty |
| 3 | 257 | 0.54 | 0.76 | 32 | empty |
| 4 | 324 | 0.53 | 0.74 | 39 | empty |
| 5 | 59 | 0.53 | 0.88 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1779 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1737 Ų buried · 15 hydrogen bonds · protein-protein
- D–L · 812 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 669 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4YPG · Structural Insights Into the Neutralization Properties of a Human Anti-Interferon… · the same entry in another collection · chain L against L, TM-score 1.00
- P01563 · AlphaFold monomer V2.0 prediction for interferon alpha-2 (P01563) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 Q6PJF2
- Every structure of UniProt P01563
- Elsewhere: RCSB PDB 4YPG · PDBe 4YPG · UniProt Q6PJF2 · UniProt P01563
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.