MolNFT v1 · #137434 · protein + DNA

Desgla-XAS195A bound to aptamer 11F7T and rivaroxaban

5VOF: “Desgla-XAS195A bound to aptamer 11F7T and rivaroxaban”. X-ray diffraction, 4 ligands (RIV, MG, NA). MolNFT v1 #137434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VOF
Type: protein + DNA
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: P00742
Ligands: RIV, MG, NA, CA

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	—	protein	231	—	P00742
L	—	protein	51	—	P00742
A	—	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.

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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