7PHX: Tsetse thrombin inhibitor

Tsetse thrombin inhibitor in complex with human alpha-thrombin - acid-stable sulfotyrosine analogue. Determined by X-ray diffraction at 1.8 Å resolution. Released 6 Oct 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Glossina morsitans morsitans
Chains: 3
Atoms: 2,590
Mol. weight: 37.65 kDa
Ligands: NAG
Released: 6 Oct 2021

Explore 7PHX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PHX contains 15 α-helices and 27 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: 12 helices, 25 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	362-365	4
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	397-399	3	3
β-strand	401-406	6	3
β-strand	411	1	6
β-strand	417	1	6
β-strand	421-425	5	3
α-helix	428-431	4
α-helix	437-438	2
β-strand	439	1	2
α-helix	440-441	2
α-helix	443-449	7
β-strand	451	1	7
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
β-strand	519	1	1
β-strand	528-532	5	2
β-strand	539-547	9	2
β-strand	548-549	2	8
β-strand	558-562	5	2
α-helix	563-566	4
α-helix	567-573	7

Chain I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	7
α-helix	24-26	3
β-strand	30-31	2	8

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	300-302	3
α-helix	309-316	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Thrombin heavy chain	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Tsetse thrombin inhibitor	I	protein	32	Glossina morsitans morsitans	O97373 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>7PHX_1 Thrombin light chain (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>7PHX_2 Thrombin heavy chain (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>7PHX_3 Tsetse thrombin inhibitor (chains I)
GEPGAPIDFDEFGDSSEEVGGTPLHEIPGIRL

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 (NA) are not listed.

Primary citation

Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues. Dowman, L.J., Agten, S.M., Ripoll-Rozada, J. et al. Chem Commun (Camb) (2021) 57:10923-10926. DOI 10.1039/d1cc04742f · 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

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