2ODY: Prothrombin

Thrombin-bound boophilin displays a functional and accessible reactive-site loop. Determined by X-ray diffraction at 2.35 Å resolution. Released 22 Jan 2008.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Bos taurus, Rhipicephalus microplus
Chains: 6
Atoms: 7,258
Mol. weight: 99.67 kDa
Ligands: NAG, PO4
Released: 22 Jan 2008

Explore 2ODY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ODY contains 45 α-helices and 62 β-strands across 6 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 A: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14C-14L	10

Chain B: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	3
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
α-helix	149C-150	4
β-strand	154	1	5
β-strand	156-163	8	2
α-helix	165-170	6
α-helix	175-176	2
β-strand	180-183	4	2
α-helix	184A-185	2
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	216	1	7
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-242	8

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14C-14H	6

Chain D: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	8
β-strand	20-21	2	9
α-helix	22-23	2
β-strand	30-35	6	10
β-strand	39-46	8	10
β-strand	51-54	4	10
α-helix	56-58	3
β-strand	60-60A	2	11
α-helix	60B-60D	3
β-strand	60F-60G	2	11
β-strand	64-68	5	10
β-strand	72	1	12
β-strand	81-83	3	10
β-strand	85-90	6	10
β-strand	95	1	13
β-strand	100	1	13
β-strand	104-108	5	10
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	9
α-helix	126-129C	7
β-strand	135-140	6	9
α-helix	149C-150	4
β-strand	154	1	12
β-strand	156-162	7	9
α-helix	165-170	6
α-helix	175-176	2
β-strand	180-183	4	9
α-helix	184A-185	2
β-strand	189	1	8
β-strand	198-202	5	9
β-strand	207-215	9	9
β-strand	216	1	14
β-strand	226-230	5	9
α-helix	232-234	3
α-helix	235-242	8

Chain E: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	7
α-helix	19-22	4
α-helix	24-25	2
β-strand	34-40	7	15
β-strand	45-51	7	15
β-strand	61	1	15
α-helix	64-71	8
α-helix	74-75	2
α-helix	85-88	4
α-helix	92-93	2
β-strand	102-108	7	16
β-strand	113-119	7	16
β-strand	129	1	16
α-helix	132-139	8

Chain F: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	14
α-helix	19-22	4
α-helix	24-25	2
β-strand	34-40	7	17
β-strand	45-51	7	17
β-strand	61	1	17
α-helix	64-71	8
α-helix	74-75	2
α-helix	85-88	4
α-helix	92-93	2
β-strand	102-108	7	18
β-strand	113-119	7	18
β-strand	129	1	18
α-helix	132-138	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin (EC 3.4.21.5)	A, C	protein	49	Bos taurus	P00735 (AlphaFold model)
Prothrombin (EC 3.4.21.5)	B, D	protein	259	Bos taurus	P00735 (AlphaFold model)
Boophilin	E, F	protein	127	Rhipicephalus microplus	Q8WPI2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2ODY_1 Prothrombin (EC 3.4.21.5) (chains A, C)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Sequence of entity 2 (B, D), FASTA

>2ODY_2 Prothrombin (EC 3.4.21.5) (chains B, D)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Sequence of entity 3 (E, F), FASTA

>2ODY_3 Boophilin (chains E, F)
QRNGFCRLPADEGICKALIPRFYFNTETGKCTMFSYGGCGGNENNFETIEECQKACGAPE
RVNDFESADFKTGCEPAADSGSCAGQLERWFYNVQSGECETFVYGGCGGNDNNYESEEEC
ELVCKNM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PO4	Phosphate ion	O4 P	4

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

Primary citation

Isolation, cloning and structural characterisation of boophilin, a multifunctional kunitz-type proteinase inhibitor from the cattle tick. Macedo-Ribeiro, S., Almeida, C., Calisto, B.M. et al. PLoS One (2008) 3:e1624-e1624. DOI 10.1371/journal.pone.0001624 · PubMed

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
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

Browse structure collections

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