Research workbench

Factor ixa superactive triple mutant, ethylene glycol-soaked

Analyse Factor ixa superactive triple mutant, ethylene glycol-soaked in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WPK
Type: protein
Length: 297 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor ixa light chain; D-phe-pro-arg-chloromethyl ketone; Coagulation factor…
EC: 3.4.21.22
UniProt: P00740
Ligands: CA
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Coagulation factor ixa light chain (EC 3.4.21.22)	protein	59	12% helix, 24% strand	P00740
L	D-phe-pro-arg-chloromethyl ketone	protein	3	0% helix, 33% strand	—
S	Coagulation factor ixa heavy chain (EC 3.4.21.22)	protein	235	11% helix, 36% strand	P00740

Ligands and binding sites

CA · Calcium ion · metal · chains S
EDO · 1,2-ethanediol · additive · chains S

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	170	0.49	0.77	25	empty
2	71	0.34	0.76	16	empty

Interfaces

2 interfaces between chains.

E–S · 814 Å² buried · 13 hydrogen bonds · protein-protein
L–S · 405 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 d-amino (disulfide, D-amino acid).

Compared structures

2WPK · factor IXa superactive triple mutant, ethylene glycol-soaked · the same entry in another collection · chain E against E, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain S 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 P00740
Elsewhere: RCSB PDB 2WPK · PDBe 2WPK · UniProt P00740

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