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SMTL ID : 8ase.1 (1 other biounit)

Crystal structure of Thrombin in complex with macrocycle T3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1:

3 residues within 4Å:

Chain B: L.46, N.53, W.92

No protein-ligand interaction detected (PLIP)

1 x NWR: (8~{S},14~{S},18~{E})-8-[(4-chlorophenyl)methyl]-3,21-dithia-7,10,16-triazatricyclo[21.2.2.1^{10,14}]octacosa-1(26),18,23(27),24-tetraene-6,9,15-trione(Non-covalent)

NWR.2:

18 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, G.238, F.239
Ligands: SO4.3

12 PLIP interactions:

12 interactions with chain B

Hydrophobic interactions: B:Y.47, B:Y.47, B:W.50, B:L.96, B:L.96, B:A.200, B:V.225, B:W.227, B:W.227
Hydrogen bonds: B:G.228, B:G.228, B:G.228

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3:

5 residues within 4Å:

Chain B: H.43, E.202, G.203, S.205
Ligands: NWR.2

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:G.203, B:S.205, B:S.205
Salt bridges: B:H.43, B:K.52

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Nielsen, A. et al., Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3. To Be Published

Release Date

2023-11-29

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

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