MolNFT v1 · #6383 · protein

Coagulation factor xa inhibitor complex

1FAX: “Coagulation factor xa inhibitor complex”. X-ray diffraction, 2 ligands (DX9, CA), 2 pockets (best druggability 0.45). MolNFT v1 #6383 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1FAX
Type: protein
Length: 290 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Factor xa
EC: 3.4.21.6
UniProt: P00742
Ligands: DX9, CA
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Factor xa (EC 3.4.21.6)	protein	235	10% helix, 37% strand	P00742
L	Factor xa (EC 3.4.21.6)	protein	55	5% helix, 22% strand	P00742

Ligands and binding sites

DX9 · (2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid · ligand · chains A
CA · Calcium ion · metal · chains A

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

Pockets

2 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	127	0.45	0.77	25	empty
2	131	0.41	0.75	30	DX9

Interfaces

1 interface between chains.

A–L · 948 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1FAX · Coagulation factor xa 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 0.98

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 1FAX · PDBe 1FAX · UniProt P00742

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