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SMTL ID : 6t7h.2 (1 other biounit)

Crystal structure of Thrombin in complex with macrocycle N14-PR4-A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1:

2 residues within 4Å:

Chain B: L.46, N.53

No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2:

8 residues within 4Å:

Chain B: S.176, T.177, W.227, G.228, E.229, K.236, Y.237, F.239

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:S.176, B:S.176, B:E.229, B:Y.237

1 x MRQ: (14S,17R)-14-(3-carbamimidamidopropyl)-3-(furan-2-ylmethyl)-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(25),7,9,21,23-pentaene-17-carboxamide(Non-covalent)

MRQ.3:

18 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, R.178, I.179, D.199, A.200, C.201, E.202, W.227, G.228, E.229, G.230, C.231, G.238

19 PLIP interactions:

19 interactions with chain B

Hydrophobic interactions: B:H.43, B:Y.47, B:W.50, B:L.96, B:I.179, B:I.179, B:W.227, B:E.229
Hydrogen bonds: B:A.200, B:E.202, B:E.202, B:G.228, B:G.230, B:G.230
Water bridges: B:S.226, B:D.232, B:F.239
Salt bridges: B:D.199
pi-Stacking: B:H.43

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

NA.4:

3 residues within 4Å:

Chain B: Y.190, R.233, K.236

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:K.236
Water bridges: B:G.198, B:D.234, B:D.234, B:G.238

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Mothukuri, G.K. et al., Macrocycle synthesis strategy based on step-wise "adding and reacting" three components enables screening of large combinatorial libraries. Chem Sci (2020)

Release Date

2020-09-30

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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