7A0E: Bovine Thrombin

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution. Determined by X-ray diffraction at 1.9 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Bos taurus, Hirudo medicinalis
Chains: 3
Atoms: 3,092
Mol. weight: 42.82 kDa
Ligands: NAG
Released: 17 Mar 2021

Explore 7A0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A0E contains 20 α-helices and 31 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: 13 helices, 22 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	77-79	3	3
β-strand	81-86	6	3
β-strand	91	1	5
β-strand	97	1	5
β-strand	101-105	5	3
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	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	6
β-strand	238-242	5	2
α-helix	244-246	3
α-helix	247-255	9

Chain III: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	6
β-strand	5	1	7
β-strand	11-12	2	8
β-strand	14-15	2	7
β-strand	21-22	2	7
β-strand	26-29	4	9
α-helix	35-37	3
β-strand	38-41	4	9
β-strand	45-46	2	8
α-helix	47-50	4
β-strand	53	1	3
α-helix	56-60	5
α-helix	61-63	3

Chain LLL: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	-1-2	4
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

>7A0E_1 Prothrombin (chains HHH)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Sequence of entity 2 (III), FASTA

>7A0E_2 Hirudin variant-1 (chains III)
VVYTDUTESGQNLULCEGSNVCGQGNKCILGSDGEKNQCVTGEGTPKPQSHNDGDFEEIP
EEYLQ

Sequence of entity 3 (LLL), FASTA

>7A0E_3 Prothrombin (chains LLL)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

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

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:

7A0D 1.6 Å, The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6…
1NL1 1.9 Å, Bovine prothrombin fragment 1 in complex with calcium ion
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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