SMTL ID : 8tqs.1

Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-mer

Ligands

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

MG.1: 7 residues within 4Å: Chain A: G.7, G.9, G.10, G.13, G.18, G.19, G.22 No protein-ligand interaction detected (PLIP)

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

NA.2: 3 residues within 4Å: Chain B: D.232, R.233, K.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.233

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 6 residues within 4Å: Chain A: T.11, A.12 Chain B: L.46, P.88, W.92 Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

1 x 4CC: N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine(Non-covalent)

4CC.4: 21 residues within 4Å: Chain B: H.43, Y.47, W.50, R.93, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, A.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.96, B:I.179, B:I.179, B:V.225, B:W.227, B:E.229 Hydrogen bonds: B:D.199, B:A.200, B:E.202

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.5: 3 residues within 4Å: Chain B: L.46, N.53 Ligands: MES.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.46 Hydrogen bonds: B:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors. Nat Commun (2024)

Release Date

2024-05-01

Peptides

Thrombin heavy chain: B
Prothrombin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
H

C
L

Thrombin heavy chain

Prothrombin

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