SMTL ID : 5vof.1

DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x RIV: 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide

RIV.1: 18 residues within 4Å: Chain A: K.82, E.83, T.84, Y.85, F.162, D.179, A.180, C.181, Q.182, V.203, S.204, W.205, G.206, E.207, G.208, G.216, I.217, Y.218 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.162, A:W.205 Hydrogen bonds: A:G.206, A:G.206, A:G.208 pi-Stacking: A:Y.85

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: Y.173, D.174, A.210, R.211, K.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.174 Water bridges: A:Y.173

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.56, N.58, Q.61, E.62, E.66 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.56, A:N.58, A:Q.61, A:E.66

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain C: A.10, C.22, U.23 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain C Metal complexes: H2O.4, H2O.4, H2O.4, C:C.22 MG.5: 5 residues within 4Å: Chain C: C.9, A.10, U.23, U.24, G.25 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunaratne, R. et al., Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat. Biotechnol. (2018)

Release Date

2018-06-13

Peptides

Coagulation factor X: A
Coagulation factor X: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Coagulation factor X

Coagulation factor X

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