Research workbench

Magacizumab Fab fragment in complex with human LRG1 epitope

Analyse Magacizumab Fab fragment in complex with human LRG1 epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q4Q
Type: protein
Length: 904 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Magacizumab light chain; Magacizumab heavy chain; LRG1 epitope
Pockets: 8 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Magacizumab light chain	protein	218	6% helix, 51% strand	—
B, D	Magacizumab heavy chain	protein	219	8% helix, 52% strand	—
E, F	LRG1 epitope	protein	15	27% helix, 0% strand	—

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, D

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

Pockets

8 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	189	0.57	0.81	40	empty
2	307	0.51	0.74	40	empty
3	101	0.48	0.80	19	empty
4	142	0.48	0.78	27	empty
5	130	0.46	0.78	20	empty

Interfaces

9 interfaces between chains.

C–D · 1883 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1871 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 505 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 410 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 409 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

7Q4Q · Magacizumab Fab fragment in complex with human LRG1 epitope · the same entry in another collection · chain A against A, 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 7Q4Q · PDBe 7Q4Q

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