MolNFT v1 · #111932 · protein
Rontalizumab Fab bound to interferon-A2
4Z5R · Interferon alpha-2: “Rontalizumab Fab bound to interferon-A2”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.76). MolNFT v1 #111932 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Z5R
- Type
- protein
- Length
- 4,354 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon alpha-2; Anti-ifn-a antibody rontalizumab light chain; Anti-ifn-a antibody…
- UniProt
- P01563
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 11 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | Interferon alpha-2 | protein | 141 | 72% helix, 0% strand | P01563 |
| J, L, V, P, R, T, A | Anti-ifn-a antibody rontalizumab light chain | protein | 217 | 6% helix, 50% strand | — |
| K, M, W, Q, S, U, B | Anti-ifn-a antibody rontalizumab heavy chain modules vh and CH1 (Fab) | protein | 213 | 7% helix, 52% strand | — |
| F | Interferon alpha-2 | protein | 140 | 72% helix, 0% strand | P01563 |
| G | Interferon alpha-2 | protein | 137 | 72% helix, 0% strand | P01563 |
| H | Interferon alpha-2 | protein | 139 | 73% helix, 0% strand | P01563 |
| I | Interferon alpha-2 | protein | 137 | 74% helix, 0% strand | P01563 |
| X | Interferon alpha-2 | protein | 137 | 74% helix, 0% strand | P01563 |
| Y | Anti-ifn-a antibody rontalizumab light chain | protein | 110 | 3% helix, 49% strand | — |
| Z | Anti-ifn-a antibody rontalizumab heavy chain modules vh and CH1 (Fab) | protein | 117 | 8% helix, 50% strand | — |
| N | Interferon alpha-2 | protein | 145 | 70% helix, 0% strand | P01563 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains J, L, F, V, W, G, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.76 | 0.79 | 101 | empty |
| 2 | 85 | 0.75 | 0.98 | 24 | empty |
| 3 | 76 | 0.73 | 0.97 | 27 | empty |
| 4 | 544 | 0.73 | 0.81 | 58 | empty |
| 5 | 74 | 0.72 | 0.97 | 27 | empty |
Interfaces
50 interfaces between chains.
- R–S · 1745 Ų buried · 15 hydrogen bonds · protein-protein
- V–W · 1724 Ų buried · 14 hydrogen bonds · protein-protein
- P–Q · 1718 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1714 Ų buried · 17 hydrogen bonds · protein-protein
- T–U · 1690 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide (disulfide).
Compared structures
- 4Z5R · Rontalizumab Fab bound to Interferon-a2 · the same entry in another collection · chain P against P, 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 P01563
- Elsewhere: RCSB PDB 4Z5R · PDBe 4Z5R · UniProt P01563
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