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Human coagulation factor ixa in complex with P-amino benzamidine

Analyse Human coagulation factor ixa in complex with P-amino benzamidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RFN
Type: protein
Length: 292 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (coagulation factor IX)
UniProt: P00740
Ligands: PBZ, CA
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	Protein (coagulation factor IX)	protein	235	12% helix, 36% strand	P00740
B	Protein (coagulation factor IX)	protein	57	9% helix, 25% strand	P00740

Ligands and binding sites

PBZ · P-amino benzamidine · ligand · chains A
CA · Calcium ion · metal · chains A
TBU · Tertiary-butyl alcohol · additive · 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	123	0.49	0.80	19	empty
2	62	0.39	0.80	19	PBZ
3	59	0.35	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 818 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

1RFN · Human coagulation factor ixa in complex with P-amino benzamidine · the same entry in another collection · chain A against A, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · 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 P00740
Elsewhere: RCSB PDB 1RFN · PDBe 1RFN · UniProt P00740

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