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SMTL ID : 8ase.2 (1 other biounit)

Crystal structure of Thrombin in complex with macrocycle T3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

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.1:

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: SO4.2

10 PLIP interactions:

10 interactions with chain B

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

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

SO4.2:

5 residues within 4Å:

Chain B: H.43, E.202, G.203, S.205
Ligands: NWR.1

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:G.203, B:D.204, B:S.205, B:S.205
Salt bridges: B:H.43

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

NAG.3:

2 residues within 4Å:

Chain B: L.46, N.53

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:N.53

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
A

B
B

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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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

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