SMTL ID : 6z48.3 (3 other biounits)

Crystal structure of Thrombin in complex with macrocycle X1vE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-1-1-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain B: Y.190, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.190, B:K.236 Water bridges: B:Y.190

1 x X1V: 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide(Non-covalent)

X1V.2: 22 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238, F.239, Y.240 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.47, B:L.96, B:I.179, B:A.200, B:W.227, B:E.229 Hydrogen bonds: B:E.202, B:G.228, B:G.228, B:G.230, B:G.230 Water bridges: B:Y.47, B:Y.47, B:D.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Habeshian, S. et al., Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale. Nat Commun (2022)

Release Date

2022-06-01

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Thrombin light chain

Thrombin heavy chain

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