MolNFT v1 · #110791 · protein

Factor xa complex with GTC000441

4Y7B · Coagulation factor X: “Factor xa complex with GTC000441”. X-ray diffraction, 2 ligands (44I, CA), 3 pockets (best druggability 0.48). MolNFT v1 #110791 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Y7B
Type: protein
Length: 287 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X
EC: 3.4.21.6
UniProt: P00742
Ligands: 44I, CA
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor X (EC 3.4.21.6)	protein	234	13% helix, 35% strand	P00742
B	Coagulation factor X (EC 3.4.21.6)	protein	53	13% helix, 30% strand	P00742

Ligands and binding sites

44I · 6-chloro-N-{(3S)-1-[(2S)-1-{(1R,5S)-7-[2-(methylamino)ethyl]-3,7-diazabicyclo[3.3.1]non-3-yl}-1-oxopropan-2-yl]-2-oxopy rrolidin-3-yl}naphthalene-2-sulfonamide · ligand · chains A
CA · Calcium ion · metal · 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	100	0.48	0.81	24	44I
2	193	0.46	0.75	26	empty
3	54	0.35	0.79	21	empty

Interfaces

1 interface between chains.

A–B · 851 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4Y7B · Factor Xa complex with GTC000441 · the same entry in another collection · chain A against A, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00742
Elsewhere: RCSB PDB 4Y7B · PDBe 4Y7B · UniProt P00742

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