2PF2: Prothrombin fragment 1

The CA+2 ion and membrane binding structure of the gla domain of ca-prothrombin fragment 1. Determined by X-ray diffraction at 2.2 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 1
Atoms: 1,317
Mol. weight: 18.31 kDa
Ligands: CA
Released: 31 Jan 1994

Explore 2PF2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PF2 contains 10 α-helices and 10 β-strands across 1 chain. 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: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	14	1
α-helix	15-19	5
α-helix	25-30	6
α-helix	36-46	11
α-helix	56-62	7
β-strand	67	1	1
β-strand	80	1	2
β-strand	81	1	3
α-helix	85	1
β-strand	86	1	2
β-strand	87	1	4
α-helix	88-89	2
β-strand	126-128	3	5
β-strand	129	1	4
β-strand	136-138	3	5
β-strand	139	1	3
α-helix	142	1
β-strand	143	1	1
α-helix	144	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin fragment 1	A	protein	156	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PF2_1 PROTHROMBIN FRAGMENT 1 (chains A)
ANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSATDAFWAKYTACESARNPREKLNE
CLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRNPDG
SITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7

Primary citation

The Ca2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. Soriano-Garcia, M., Padmanabhan, K., de Vos, A.M. et al. Biochemistry (1992) 31:2554-2566. DOI 10.1021/bi00124a016 · 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…
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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