MolNFT v1 · #53277 · protein

Factor ixa superactive mutant, egr-cmk inhibited

2WPM · Coagulation factor ixa light chain: “Factor ixa superactive mutant, egr-cmk inhibited”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.50). MolNFT v1 #53277 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2WPM
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; Glu-gly-arg-chloromethyl ketone; Coagulation factor…
EC: 3.4.21.22
UniProt: P00740
Ligands: CA
Pockets: 2 · best druggability 0.50

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	7% helix, 27% strand	P00740
L	Glu-gly-arg-chloromethyl ketone	protein	3	0% helix, 33% strand	—
S	Coagulation factor ixa heavy chain (EC 3.4.21.22)	protein	235	12% helix, 36% strand	P00740

Ligands and binding sites

CA · Calcium ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.50	0.77	24	empty
2	62	0.31	0.75	19	empty

Interfaces

2 interfaces between chains.

E–S · 811 Å² buried · 9 hydrogen bonds · protein-protein
L–S · 377 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

2WPM · factor IXa superactive mutant, EGR-CMK inhibited · 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 0.97

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 2WPM · PDBe 2WPM · UniProt P00740

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