MolNFT v1 · #164888 · protein

Crystal structure of the omalizumab Fab LEU158PRO light chain mutant - crystal form I

6TCO: “Crystal structure of the omalizumab Fab LEU158PRO light chain mutant - crystal form I”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.69). MolNFT v1 #164888 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6TCO
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Omalizumab Fab LEU158PRO light chain mutant
Ligands: SO4
Pockets: 6 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Omalizumab Fab LEU158PRO light chain mutant	protein	216	6% helix, 54% strand	—
H, B	Omalizumab Fab LEU158PRO light chain mutant	protein	215	9% helix, 50% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains L, H, A, B
EDO · 1,2-ethanediol · additive · 18 copies · chains L, H, A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	753	0.69	0.76	78	EDO
2	77	0.54	0.86	24	EDO
3	126	0.51	0.81	27	EDO
4	301	0.51	0.73	38	empty
5	112	0.41	0.76	22	empty

Interfaces

5 interfaces between chains.

A–B · 1768 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1753 Å² buried · 13 hydrogen bonds · protein-protein
H–A · 140 Å² buried · 1 hydrogen bond · protein-protein
L–A · 91 Å² buried · 1 hydrogen bond · protein-protein
H–B · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6TCO · Crystal structure of the omalizumab Fab Leu158Pro light chain mutant - crystal form I · the same entry in another collection · chain L against L, 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 6TCO · PDBe 6TCO

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.