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Factor xa - cation

Analyse Factor xa - cation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BOK
Type: protein
Length: 271 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X
EC: 3.4.21.6
UniProt: P00742
Ligands: 784, NA
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor X (EC 3.4.21.6)	protein	222	14% helix, 36% strand	P00742
L	Coagulation factor X (EC 3.4.21.6)	protein	49	8% helix, 24% strand	P00742

Ligands and binding sites

784 · [amino (4-{(3as,4r,8as,8br)-1,3-dioxo-2- [3-(trimethylammonio) propyl]decahydropyrrolo[3,4-A] pyrrolizin-4-yl}phenyl) methylene]ammonium · ligand · chains A
NA · Sodium ion · metal · chains A

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

Pockets

4 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	138	0.47	0.78	27	784
2	180	0.45	0.75	28	empty
3	82	0.36	0.76	27	empty
4	51	0.29	0.75	13	empty

Interfaces

1 interface between chains.

A–L · 850 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2BOK · Factor Xa - cation · 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 0.98

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 2BOK · PDBe 2BOK · UniProt P00742

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