1NL2: Bovine prothrombin fragment 1

Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine. Determined by X-ray diffraction at 2.3 Å resolution. Released 16 Sept 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Bos taurus
Chains: 1
Atoms: 1,323
Mol. weight: 18.38 kDa
Ligands: LPS, CA, NAG
Released: 16 Sept 2003

Explore 1NL2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NL2 contains 11 α-helices and 11 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-12	2
α-helix	14	1
α-helix	15-19	5
α-helix	25-31	7
α-helix	35-46	12
α-helix	49-51	3
α-helix	55-63	9
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	116	1	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	A	protein	146	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1NL2_1 Prothrombin (chains A)
ANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSATDAFWAKYTACESARNPREKLNE
CLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRNPDG
SITGPWCYTTSPTLRREECSVPVCGQ

Ligands and cofactors

ID	Name	Formula	Copies
LPS	O-{HYDROXY[((2R)-2-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propyl)oxy]phosphor…	C21 H44 N O9 P	1
CA	Calcium ion	Ca	7
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Huang, M., Rigby, A.C., Morelli, X. et al. Nat Struct Biol (2003) 10:751-756. DOI 10.1038/nsb971 · 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…
2ODY 2.35 Å, Thrombin-bound boophilin displays a functional and accessible reactive-site loop

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