Research workbench

Crystal structure of egrck-inhibited gla-domainless fixa (K148Q, R150Q variant)

Analyse Crystal structure of egrck-inhibited gla-domainless fixa (K148Q, R150Q variant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RFK
Type: protein
Length: 300 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor IX; Glu-gly-AR7-0QE
EC: 3.4.21.22
UniProt: P00740
Ligands: CA, 0QE
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Coagulation factor IX (EC 3.4.21.22)	protein	62	6% helix, 26% strand	P00740
S	Coagulation factor IX (EC 3.4.21.22)	protein	235	13% helix, 37% strand	P00740
I	Glu-gly-AR7-0QE	protein	3	0% helix, 33% strand	—

Ligands and binding sites

CA · Calcium ion · metal · chains S
0QE · Chloromethane · ion · chains S, I
GOL · Glycerol · additive · 10 copies · chains E, S
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains E, S

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.46	0.77	21	empty

Interfaces

2 interfaces between chains.

E–S · 808 Å² buried · 6 hydrogen bonds · protein-protein
S–I · 368 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

6RFK · Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) · 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 6RFK · PDBe 6RFK · UniProt P00740

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.