6TKL: Non-cleavable tsetse thrombin inhibitor

Non-cleavable tsetse thrombin inhibitor in complex with human alpha-thrombin. Determined by X-ray diffraction at 1.3 Å resolution. Released 4 Nov 2020.

Method: X-ray diffraction
Resolution: 1.3 Å
Organisms: Homo sapiens, Glossina morsitans morsitans
Chains: 3
Atoms: 2,844
Mol. weight: 40.19 kDa
Ligands: NAG
Released: 4 Nov 2020

Explore 6TKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TKL contains 16 α-helices and 28 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	322	1	1
β-strand	325-326	2	2
α-helix	327-328	2
β-strand	335-340	6	3
β-strand	345-352	8	3
β-strand	357-360	4	3
α-helix	362-364	3
β-strand	366-367	2	4
α-helix	368-370	3
β-strand	372-373	2	4
α-helix	376-378	3
β-strand	379-383	5	3
β-strand	387	1	5
β-strand	397-406	10	3
β-strand	411	1	6
β-strand	417	1	6
β-strand	421-425	5	3
α-helix	428-431	4
β-strand	432	1	7
β-strand	435	1	7
α-helix	437-438	2
β-strand	439	1	2
α-helix	440-441	2
α-helix	443-449	7
β-strand	451	1	8
β-strand	455-460	6	2
β-strand	479	1	5
β-strand	481-487	7	2
α-helix	490-495	6
α-helix	500-501	2
β-strand	505-508	4	2
α-helix	512-514	3
β-strand	519	1	1
β-strand	528-532	5	2
β-strand	539-547	9	2
β-strand	548-549	2	9
β-strand	558-562	5	2
α-helix	564-566	3
α-helix	567-577	11

Chain I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	8
α-helix	24-26	3
β-strand	30-31	2	9

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	300-302	3
α-helix	309-315	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Prothrombin	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Tsetse thrombin inhibitor	I	protein	53	Glossina morsitans morsitans	O97373 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6TKL_1 Prothrombin (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>6TKL_2 Prothrombin (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>6TKL_3 Tsetse thrombin inhibitor (chains I)
MKFFTVLFFLLSIIYLIVAAPGEPGAPIDYDEYGDSSEEVGGTPLHEIPGIRL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, NA) are not listed.

Primary citation

Sulfotyrosine-Mediated Recognition of Human Thrombin by a Tsetse Fly Anticoagulant Mimics Physiological Substrates. Calisto, B.M., Ripoll-Rozada, J., Dowman, L.J. et al. Cell Chem Biol (2021) 28:26. DOI 10.1016/j.chembiol.2020.10.002 · PubMed

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

Browse structure collections

About this viewer

MolViewer shows 6TKL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.