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Factor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-CARBAMIDOYL-PHENYL)-N-PHENETHYL-PROPIONIC ACID AMIDE

Analyse Factor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-CARBAMIDOYL-PHE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LIW
Type: protein
Length: 285 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.22
Source: Homo sapiens
Molecule: Activated factor Xa heavy chain; Factor X light chain
EC: 3.4.21.6
UniProt: P00742
Ligands: RUP, CA
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · resolution 2.22 · 2 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Activated factor Xa heavy chain (EC 3.4.21.6)	protein	234	13% helix, 37% strand	P00742
B	Factor X light chain (EC 3.4.21.6)	protein	51	8% helix, 27% strand	P00742

Ligands and binding sites

RUP · (R)-2-(3-adamantan-1-yl-ureido)-3-(3-carbamimidoyl-phenyl)-N-phenethyl-propionamide · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.45	0.79	24	RUP
2	126	0.43	0.76	26	empty
3	56	0.34	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 943 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3LIW · Factor xa in complex with (R)-2-(1-adamantylcarbamoylamino)… · the same entry in another collection · chain A against A, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00742
Elsewhere: RCSB PDB 3LIW · PDBe 3LIW · UniProt P00742

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