1YCP: Fibrinogen-aa peptide 1-23

The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of phe-8 to tyrosine strongly inhibits normal cleavage at arginine-16. Determined by X-ray diffraction at 2.5 Å resolution. Released 6 May 1998.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Bos taurus
Chains: 7
Atoms: 4,846
Mol. weight: 75.73 kDa
Released: 6 May 1998

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

Secondary structure: helices and β-sheets

1YCP contains 26 α-helices and 51 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 F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	315	1	2

Chain H: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	31-35	5	3
β-strand	39-44	6	3
β-strand	45-46	2	4
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	60-60A	2	5
α-helix	60B-60D	3
β-strand	60F-60G	2	5
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	6
β-strand	81-83	3	3
β-strand	85-90	6	4
β-strand	95	1	7
β-strand	100	1	7
β-strand	104-108	5	4
β-strand	115	1	8
β-strand	118	1	8
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	6
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
α-helix	175-176	2
β-strand	180-183	4	2
α-helix	186-186B	3
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-216	10	2
β-strand	226-230	5	2
α-helix	231-241	11

Chain J: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	14C-14K	9

Chain K: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	9
α-helix	20	1
β-strand	21	1	10
α-helix	22-23	2
β-strand	30-35	6	11
β-strand	39-46	8	11
β-strand	51-54	4	11
α-helix	56-59	4
β-strand	60-60A	2	12
α-helix	60B-60D	3
β-strand	60F-60G	2	12
α-helix	61-63	3
β-strand	64-67	4	11
β-strand	68	1	13
β-strand	72	1	14
β-strand	81	1	13
β-strand	85-90	6	11
β-strand	95	1	15
β-strand	100	1	15
β-strand	104-108	5	11
β-strand	122	1	10
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	10

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14H	6

Chain M: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	154	1	14
β-strand	156-162	7	10
α-helix	163-164	2
α-helix	165-171	7
β-strand	182-183	2	10
α-helix	186-186B	3
β-strand	189	1	9
β-strand	198-203	6	10
β-strand	206-215	10	10
β-strand	226-230	5	10
α-helix	235-240	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epsilon thrombin	J, L	protein	49	Bos taurus	P00735 (AlphaFold model)
Alpha thrombin	H	protein	259	Bos taurus	P00735 (AlphaFold model)
Fibrinopeptide a-alpha	F, N	protein	23		P02671 (AlphaFold model)
Epsilon thrombin	K	protein	150	Bos taurus	P00735 (AlphaFold model)
Epsilon thrombin	M	protein	109	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (J, L), FASTA

>1YCP_1 EPSILON THROMBIN (chains J, L)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Sequence of entity 2 (H), FASTA

>1YCP_2 ALPHA THROMBIN (chains H)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Sequence of entity 3 (F, N), FASTA

>1YCP_3 FIBRINOPEPTIDE A-ALPHA (chains F, N)
ADSGEGDYLAEGGGVRGPRVVER

Sequence of entity 4 (K), FASTA

>1YCP_4 EPSILON THROMBIN (chains K)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTT

Sequence of entity 5 (M), FASTA

>1YCP_5 EPSILON THROMBIN (chains M)
SVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFV
MKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Primary citation

Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16. Malkowski, M.G., Martin, P.D., Lord, S.T. et al. Biochem J (1997) 326:815-822. 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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