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Rontalizumab Fab bound to interferon-A2

Analyse Rontalizumab Fab bound to interferon-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 15 hydrogen bonds · protein-protein
V–W · 1724 Å² buried · 14 hydrogen bonds · protein-protein
P–Q · 1718 Å² buried · 17 hydrogen bonds · protein-protein
J–K · 1714 Å² buried · 17 hydrogen bonds · protein-protein
T–U · 1690 Å² 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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