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Epidermal growth factor-like domain from human factor IX

Analyse Epidermal growth factor-like domain from human factor IX in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EDM
Type: protein
Length: 78 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Factor IX
UniProt: P00740
Ligands: CA

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C	Factor IX	protein	39	0% helix, 26% strand	P00740

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains B, C

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

Interfaces

1 interface between chains.

B–C · 398 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1EDM · Epidermal growth factor-like domain from human factor IX · the same entry in another collection · chain C against C, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 1EDM · PDBe 1EDM · UniProt P00740

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