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factor Xa in complex with the dual thrombin-FXa inhibitor 58.

Analyse factor Xa in complex with the dual thrombin-FXa inhibitor 58. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BTI
Type: protein
Length: 574 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: HOMO SAPIENS
Molecule: Coagulation factor X heavy chain; Coagulation factor X light chain
EC: 3.4.21.6
UniProt: P00742
Ligands: 7R9, CA
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · resolution 2.3 · 2 distinct chains · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Coagulation factor X heavy chain (EC 3.4.21.6)	protein	53	13% helix, 26% strand	P00742
B, F	Coagulation factor X light chain (EC 3.4.21.6)	protein	234	13% helix, 38% strand	P00742

Ligands and binding sites

7R9 · 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide · ligand · 2 copies · chains B, F
CA · Calcium ion · metal · 2 copies · chains B, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	936	0.74	0.78	93	empty
2	173	0.49	0.77	27	empty
3	103	0.46	0.80	24	7R9
4	99	0.45	0.79	21	7R9

Interfaces

5 interfaces between chains.

A–B · 918 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 906 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 354 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 229 Å² buried · 2 hydrogen bonds · protein-protein
B–F · 113 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4BTI · Factor xa in complex with the dual thrombin-fxa inhibitor 58. · the same entry in another collection · chain F against F, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain B 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 4BTI · PDBe 4BTI · UniProt P00742

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