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Desgla-XAS195A bound to aptamer 11F7T and rivaroxaban

Analyse Desgla-XAS195A bound to aptamer 11F7T and rivaroxaban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VOF
Type: protein + DNA
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor X; DNA/RNA (36-mer)
EC: 3.4.21.6
UniProt: P00742
Ligands: RIV, MG, NA, CA
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Coagulation factor X (EC 3.4.21.6)	protein	231	13% helix, 36% strand	P00742
L	Coagulation factor X (EC 3.4.21.6)	protein	51	8% helix, 31% strand	P00742
A	DNA/RNA (36-mer)	dna	36	—	—

Ligands and binding sites

RIV · 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl) phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide · ligand · chains H
MG · Magnesium ion · metal · 2 copies · chains A
NA · Sodium ion · metal · chains H
CA · Calcium ion · metal · chains H

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

Pockets

4 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	180	0.51	0.79	20	MG
2	106	0.46	0.79	25	RIV
3	92	0.40	0.77	18	empty
4	99	0.36	0.76	15	empty

Interfaces

2 interfaces between chains.

H–L · 899 Å² buried · 11 hydrogen bonds · protein-protein
H–A · 729 Å² buried · 15 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 19 modified, 8 disulfide (nucleotide modification, disulfide).

Compared structures

5VOF · DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban · the same entry in another collection · chain H against H, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain H 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 5VOF · PDBe 5VOF · UniProt P00742

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