MolNFT v1 · #109603 · protein

Structure of omalizumab Fab fragment crystal form 1

4X7S · Epididymis luminal protein 214: “Structure of omalizumab Fab fragment crystal form 1”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #109603 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X7S
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epididymis luminal protein 214; Ig kappa chain C region
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Epididymis luminal protein 214	protein	222	8% helix, 50% strand	—
L	Ig kappa chain C region	protein	218	6% helix, 54% strand	—

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	606	0.62	0.74	62	empty
2	233	0.55	0.78	39	empty
3	51	0.49	0.87	20	empty
4	53	0.26	0.74	21	empty
5	51	0.25	0.73	14	empty

Interfaces

1 interface between chains.

H–L · 1928 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4X7S · Structure of omalizumab Fab fragment crystal form 1 · 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 4X7S · PDBe 4X7S

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