1ID5: Thrombin

Crystal structure of bovine thrombin complex with protease inhibitor ecotin. Determined by X-ray diffraction at 2.5 Å resolution. Released 5 Sept 2001.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Bos taurus, Escherichia coli
Chains: 3
Atoms: 3,486
Mol. weight: 51.56 kDa
Ligands: CA
Released: 5 Sept 2001

Explore 1ID5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ID5 contains 19 α-helices and 29 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, 18 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	64-68	5	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	104-108	5	3
α-helix	111-114	4
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	4
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	2
α-helix	184-185	2
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	231-234	4
α-helix	235-243	9

Chain I: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	13-16	4
β-strand	20-25	6	2
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-47	12	5
β-strand	53-54	2	2
β-strand	55	1	6
β-strand	56-64	9	2
β-strand	69-83	15	2
β-strand	94-98	5	5
β-strand	99	1	6
α-helix	102-105	4
β-strand	106-108	3	5
α-helix	109	1
β-strand	115-120	6	2
β-strand	124-131	8	5
α-helix	132-133	2

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
Thrombin	L	protein	49	Bos taurus	P00735 (AlphaFold model)
Thrombin	H	protein	256	Bos taurus	P00735 (AlphaFold model)
Ecotin	I	protein	142	Escherichia coli	P23827 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1ID5_1 THROMBIN (chains L)
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Sequence of entity 2 (H), FASTA

>1ID5_2 THROMBIN (chains H)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDR

Sequence of entity 3 (I), FASTA

>1ID5_3 ECOTIN (chains I)
AESVQPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLE
NKTLEGWGYDYYVFDKVSSPVSTRMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTP
DNVDVKYRVWKAEEKIDNAVVR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

Primary citation

Crystal structure of thrombin-ecotin reveals conformational changes and extended interactions. Wang, S.X., Esmon, C.T., Fletterick, R.J. Biochemistry (2001) 40:10038-10046. DOI 10.1021/bi010712h · 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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