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An antidote for dabigatran

Analyse An antidote for dabigatran in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JN1
Type: protein
Length: 444 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-dabigatran FAB1, heavy chain; Anti-dabigatran FAB1, light chain
Pockets: 4 · best druggability 0.67

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-dabigatran FAB1, heavy chain	protein	225	9% helix, 52% strand	—
L	Anti-dabigatran FAB1, light chain	protein	219	5% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 8 copies · chains H, L

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

Pockets

4 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	720	0.67	0.75	59	empty
2	64	0.52	0.86	16	empty
3	85	0.50	0.83	21	GOL
4	126	0.42	0.76	25	empty

Interfaces

1 interface between chains.

H–L · 2023 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4JN1 · An Antidote for Dabigatran · 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 4JN1 · PDBe 4JN1

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