MolNFT v1 · #54964 · protein

Factor xa - cation inhibitor complex

2Y5G · Activated factor xa heavy chain: “Factor xa - cation inhibitor complex”. X-ray diffraction, 2 ligands (FJD, NA), 3 pockets (best druggability 0.49). MolNFT v1 #54964 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Y5G
Type: protein
Length: 287 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Activated factor xa heavy chain; Factor X light chain
EC: 3.4.21.6
UniProt: P00742
Ligands: FJD, NA
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Activated factor xa heavy chain (EC 3.4.21.6)	protein	233	13% helix, 36% strand	P00742
L	Factor X light chain (EC 3.4.21.6)	protein	54	7% helix, 26% strand	P00742

Ligands and binding sites

FJD · 3-[(3as,4r,5s,8as,8br)-4-[5-(5-chlorothiophen-2-yl)-1,3-oxazol-2-yl]-1,3-dioxo-4,6,7,8,8A,8B-hexahydro-3AH-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium · ligand · chains A
NA · Sodium 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	172	0.49	0.77	30	FJD
2	109	0.42	0.77	24	empty
3	50	0.30	0.76	14	empty

Interfaces

1 interface between chains.

A–L · 931 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2Y5G · Factor xa - cation inhibitor complex · 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 2Y5G · PDBe 2Y5G · UniProt P00742

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