MolNFT v1 · #109604 · protein

Structure of omalizumab Fab fragment, crystal form 2

4X7T · Omalizumab-Fab heavy chain: “Structure of omalizumab Fab fragment, crystal form 2”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.83). MolNFT v1 #109604 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4X7T
Type: protein
Length: 880 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Omalizumab-Fab heavy chain; Omalizumab-Fab light chain
Ligands: SO4
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Omalizumab-Fab heavy chain	protein	222	8% helix, 50% strand	—
L, B	Omalizumab-Fab light chain	protein	218	6% helix, 55% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains H, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.83	0.85	88	empty
2	286	0.59	0.78	38	empty
3	455	0.58	0.74	50	empty
4	59	0.57	0.90	21	empty
5	269	0.56	0.77	39	empty

Interfaces

5 interfaces between chains.

A–B · 1934 Å² buried · 18 hydrogen bonds · protein-protein
H–L · 1888 Å² buried · 16 hydrogen bonds · protein-protein
L–B · 653 Å² buried · 10 hydrogen bonds · protein-protein
H–B · 226 Å² buried · 1 hydrogen bond · protein-protein
L–A · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4X7T · Structure of Omalizumab Fab fragment, crystal form 2 · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 4X7T · PDBe 4X7T

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