1YPK: Thrombin Inhibitor Complex

Thrombin Inhibitor Complex. Determined by X-ray diffraction at 1.78 Å resolution. Released 17 Jan 2006.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, Hirudo medicinalis
Chains: 3
Atoms: 2,598
Mol. weight: 34.75 kDa
Ligands: CCR
Released: 17 Jan 2006

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

Secondary structure: helices and β-sheets

1YPK contains 17 α-helices and 22 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: 13 helices, 22 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	111-114	4
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	154	1	5
β-strand	156-162	7	2
α-helix	165-170	6
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	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-244	10

Chain I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	7-9	3

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14I	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin light chain	L	protein	27	Homo sapiens	P00734 (AlphaFold model)
Prothrombin heavy chain	H	protein	257	Homo sapiens	P00734 (AlphaFold model)
10-mer peptide from Acety-Hirudin(54-65) sulfated	I	protein	10	Hirudo medicinalis	P01050 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YPK_1 Prothrombin light chain (chains L)
ADCGLRPLFEKKSLEDKTERELLESYI

Sequence of entity 2 (H), FASTA

>1YPK_2 Prothrombin heavy chain (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQF

Sequence of entity 3 (I), FASTA

>1YPK_3 10-mer peptide from Acety-Hirudin(54-65) sulfated (chains I)
DFEEIPEEYL

Ligands and cofactors

ID	Name	Formula	Copies
CCR	[n-[N-(4-methoxy-2,3,6-trimethylphenylsulfonyl)-L-aspartyl]-D-(4-amidino-phenyl…	C29 H39 N5 O7 S	1

Primary citation

A Simple Protocol To Estimate Differences in Protein Binding Affinity for Enantiomers without Prior Resolution of Racemates. Fokkens, J., Klebe, G. Angew Chem Int Ed Engl (2006) 45:985-989. DOI 10.1002/anie.200502302 · PubMed

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

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