1MKW: Alpha-thrombin

The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the yppw segment and active site residues upon ligand binding. Determined by X-ray diffraction at 2.3 Å resolution. Released 7 Jul 1997.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Bos taurus
Chains: 3
Atoms: 4,838
Mol. weight: 71 kDa
Released: 7 Jul 1997

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

Secondary structure: helices and β-sheets

1MKW contains 24 α-helices and 45 β-strands across 3 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 H: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-36	7	3
β-strand	38-46	9	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	64-69	6	3
α-helix	77A-79	3
β-strand	80-83	4	3
β-strand	85-90	6	3
β-strand	95	1	5
β-strand	100	1	5
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
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	207-215	9	2
β-strand	226-230	5	2
α-helix	235-242	8

Chain K: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14J	8
β-strand	19-21	3	6
α-helix	22-23	2
β-strand	30-35	6	7
β-strand	39-46	8	7
β-strand	51-54	4	7
α-helix	56-58	3
β-strand	60-60A	2	8
α-helix	60B-60D	3
β-strand	60F-60G	2	8
β-strand	64-68	5	7
β-strand	72	1	9
β-strand	81-90	10	7
β-strand	95	1	10
β-strand	100	1	10
β-strand	104-108	5	7
β-strand	115	1	11
β-strand	118	1	11
α-helix	120-121	2
β-strand	122	1	6
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	6
β-strand	154	1	9
β-strand	156-161	6	6
β-strand	162	1	12
α-helix	165-170	6
β-strand	180-183	4	12
α-helix	184A-185	2
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	213	1	12
β-strand	226-229	4	12
α-helix	232-234	3
α-helix	235-242	8

Chain L: 2 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-thrombin	L	protein	49	Bos taurus	P00735 (AlphaFold model)
Alpha-thrombin	H	protein	259	Bos taurus	P00735 (AlphaFold model)
Prethrombin-2	K	protein	308	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1MKW_1 ALPHA-THROMBIN (chains L)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Sequence of entity 2 (H), FASTA

>1MKW_2 ALPHA-THROMBIN (chains H)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Sequence of entity 3 (K), FASTA

>1MKW_3 PRETHROMBIN-2 (chains K)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGL
SPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRY
ERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLH
AGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYK
PGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQ
KVIDRLGS

Primary citation

The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding. Malkowski, M.G., Martin, P.D., Guzik, J.C. et al. Protein Sci (1997) 6:1438-1448. 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…
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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