7A0D: Bovine Thrombin

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution. Determined by X-ray diffraction at 1.6 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Bos taurus, Hirudo medicinalis
Chains: 3
Atoms: 3,207
Mol. weight: 43.02 kDa
Released: 17 Mar 2021

Explore 7A0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A0D contains 19 α-helices and 35 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 HHH: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	5-6	2	2
α-helix	7-8	2
β-strand	15-20	6	3
β-strand	25-32	8	3
β-strand	37-40	4	3
α-helix	42-44	3
β-strand	46-47	2	4
α-helix	48-50	3
β-strand	52-53	2	4
α-helix	56-58	3
β-strand	59-63	5	3
β-strand	67	1	5
β-strand	77-79	3	3
β-strand	81-86	6	3
β-strand	91	1	6
β-strand	97	1	6
β-strand	101-105	5	3
α-helix	108-111	4
β-strand	112	1	7
β-strand	115	1	7
α-helix	117-118	2
β-strand	119	1	2
α-helix	120-121	2
α-helix	123-129	7
β-strand	135-140	6	2
α-helix	152-155	4
β-strand	159	1	5
β-strand	161-167	7	2
α-helix	170-175	6
α-helix	180-181	2
β-strand	185-188	4	2
α-helix	190-191	2
β-strand	199	1	1
β-strand	208-212	5	2
β-strand	219-227	9	2
β-strand	228-229	2	8
β-strand	238-242	5	2
α-helix	244-246	3
α-helix	247-255	9

Chain III: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
β-strand	5	1	9
β-strand	11-12	2	10
β-strand	14-17	4	9
β-strand	20-22	3	9
β-strand	26-29	4	11
α-helix	35-37	3
β-strand	38-41	4	11
β-strand	45-46	2	10
α-helix	47-52	6
β-strand	53	1	3
α-helix	57-60	4

Chain LLL: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	25-33	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	HHH	protein	259	Bos taurus	P00735 (AlphaFold model)
Hirudin variant-1	III	protein	65	Hirudo medicinalis	P01050 (AlphaFold model)
Prothrombin	LLL	protein	49	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (HHH), FASTA

>7A0D_1 Prothrombin (chains HHH)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Sequence of entity 2 (III), FASTA

>7A0D_2 Hirudin variant-1 (chains III)
VVYTDCTESGQNLCLUEGSNVCGQGNKUILGSDGEKNQCVTGEGTPKPQSHNDGDFEEIP
EEYLQ

Sequence of entity 3 (LLL), FASTA

>7A0D_3 Prothrombin (chains LLL)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Primary citation

Diselenide crosslinks for enhanced and simplified oxidative protein folding. Mousa, R., Hidmi, T., Pomyalov, S. et al. Commun Chem (2021) 4:30. DOI 10.1038/s42004-021-00463-9

Other PDB entries of the same protein (UniProt P00735 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NL1 1.9 Å, Bovine prothrombin fragment 1 in complex with calcium ion
7A0E 1.9 Å, The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9…
1ETR 2.2 Å, Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the…
1MKX 2.2 Å, The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement…
1UCY 2.2 Å, Thrombin complexed with fibrinopeptide a alpha (residues 7-19). Three complexes, one…
2PF2 2.2 Å, The CA+2 ion and membrane binding structure of the gla domain of ca-prothrombin fragment 1
3PMA 2.2 Å, 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose…
1BBR 2.3 Å, The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine…
1ETS 2.3 Å, Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the…
1MKW 2.3 Å, The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement…
1NL2 2.3 Å, Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine
2ODY 2.35 Å, Thrombin-bound boophilin displays a functional and accessible reactive-site loop

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