1UCY: Thrombin

Thrombin complexed with fibrinopeptide a alpha (residues 7-19). Three complexes, one with epsilon-thrombin and two with alpha-thrombin. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Feb 1997.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 10
Atoms: 8,184
Mol. weight: 110.61 kDa
Released: 12 Feb 1997

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

Secondary structure: helices and β-sheets

1UCY contains 37 α-helices and 69 β-strands across 10 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 E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-170	6
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	231-242	12

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	14-15	2	2

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	14-15	2	8

Chain H: 7 helices, 15 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
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	3
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

Chain I: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	14-15	2	15

Chain J: 2 helices, 0 β-strands

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

Chain K: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	7
β-strand	20-21	2	8
α-helix	22-23	2
β-strand	30-35	6	9
β-strand	40-46	7	9
β-strand	51-54	4	9
α-helix	56-58	3
β-strand	60-60A	2	10
α-helix	60B-60D	3
β-strand	60F-60G	2	10
α-helix	61-63	3
β-strand	64-68	5	9
β-strand	72	1	11
β-strand	81-90	10	9
β-strand	95	1	12
β-strand	100	1	12
β-strand	104-108	5	9
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	8
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	8
β-strand	149B	1	13
β-strand	149D	1	13
β-strand	154	1	11
β-strand	156-162	7	8
α-helix	165-171	7
β-strand	180-183	4	8
β-strand	189	1	7
β-strand	198-202	5	8
β-strand	207-216	10	8
β-strand	226-230	5	8
α-helix	231-234	4
α-helix	235-242	8

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14C-14H	6

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin	J, L, M	protein	49	Bos taurus	P00735 (AlphaFold model)
Thrombin	H	protein	150	Bos taurus	P00735 (AlphaFold model)
Thrombin	E	protein	109	Bos taurus	P00735 (AlphaFold model)
Fibrinopeptide a-alpha	F, G, I	protein	13		P68108 (AlphaFold model)
Thrombin	K, N	protein	259	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (J, L, M), FASTA

>1UCY_1 THROMBIN (chains J, L, M)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Sequence of entity 2 (H), FASTA

>1UCY_2 THROMBIN (chains H)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTT

Sequence of entity 3 (E), FASTA

>1UCY_3 THROMBIN (chains E)
SVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFV
MKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Sequence of entity 4 (F, G, I), FASTA

>1UCY_4 FIBRINOPEPTIDE A-ALPHA (chains F, G, I)
XDFLAEGGGVRPR

Sequence of entity 5 (K, N), FASTA

>1UCY_5 THROMBIN (chains K, N)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Primary citation

Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues. Martin, P.D., Malkowski, M.G., DiMaio, J. et al. Biochemistry (1996) 35:13030-13039. DOI 10.1021/bi960656y · 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…
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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