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Crystal structure of FXA/SELECTIDE/NAPC2 ternary complex

Analyse Crystal structure of FXA/SELECTIDE/NAPC2 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H9E
Type: protein
Length: 338 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X heavy chain; Coagulation factor X light chain; Anti-coagulant…
EC: 3.4.21.6
UniProt: P00742, Q16938
Ligands: NA, PO4
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Coagulation factor X heavy chain (EC 3.4.21.6)	protein	233	13% helix, 38% strand	P00742
L	Coagulation factor X light chain (EC 3.4.21.6)	protein	48	6% helix, 33% strand	P00742
C	Anti-coagulant protein C2	protein	52	15% helix, 25% strand	Q16938
S	Selectide inhibitor dty-ile-arg-leu-lpd peptide	protein	5	0% helix, 20% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains H
PO4 · Phosphate ion · ion · 6 copies · chains H, L
ACT · Acetate ion · additive · 3 copies · chains H

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	218	0.48	0.74	28	empty
2	71	0.35	0.77	21	empty

Interfaces

3 interfaces between chains.

H–C · 1101 Å² buried · 27 hydrogen bonds · protein-protein
H–L · 803 Å² buried · 10 hydrogen bonds · protein-protein
H–S · 549 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).

Compared structures

2H9E · Crystal Structure of FXa/selectide/NAPC2 ternary complex · the same entry in another collection · chain H against H, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain H 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
Every structure of UniProt Q16938
Elsewhere: RCSB PDB 2H9E · PDBe 2H9E · UniProt P00742 · UniProt Q16938

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