MolNFT v1 · #123951 · protein

Human factor xa in complex with synthetic inhibitor benzylsulfonyl- DSER(BENZYL)-gly-4-amidinobenzylamide

5K0H · Coagulation factor X: “Human factor xa in complex with synthetic inhibitor benzylsulfonyl- DSER(BENZYL)-gly-4-amidinobenzylamide”. X-ray diffraction, 2 ligands (6PK, CA), 3 pockets (best druggability 0.46). MolNFT v1 #123951 on…

PDB: 5K0H
Type: protein
Length: 285 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: 6PK, CA
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor X (EC 3.4.21.6)	protein	234	13% helix, 36% strand	P00742
B	Coagulation factor X (EC 3.4.21.6)	protein	51	8% helix, 31% strand	P00742

Ligands and binding sites

6PK · O-benzyl-N-(benzylsulfonyl)-D-seryl-N-[(4-carbamimidoylphenyl)methyl]glycinamide · ligand · chains A
CA · Calcium ion · metal · 2 copies · 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	145	0.46	0.76	26	empty
2	105	0.44	0.78	25	6PK
3	51	0.28	0.75	12	empty

Interfaces

1 interface between chains.

A–B · 899 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5K0H · Human factor Xa in complex with synthetic inhibitor… · 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 5K0H · PDBe 5K0H · UniProt P00742

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