1NY2: Thrombin light chain

Human alpha thrombin inhibited by RPPGF and hirugen. Determined by X-ray diffraction at 2.3 Å resolution. Released 4 Mar 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,554
Mol. weight: 35.81 kDa
Released: 4 Mar 2003

Explore 1NY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NY2 contains 11 α-helices and 28 β-strands across 2 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 1: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1F	1	1
α-helix	8-10	3
α-helix	14D-14G	4

Chain 2: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	2
β-strand	20-21	2	3
β-strand	30-36	7	4
β-strand	38-46	9	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	4
β-strand	72	1	6
β-strand	81-90	10	4
β-strand	95	1	7
β-strand	100	1	7
β-strand	104-108	5	4
α-helix	111-114	4
β-strand	115	1	8
β-strand	118	1	8
β-strand	122	1	3
β-strand	123	1	1
α-helix	124-125	2
α-helix	126-129C	7
β-strand	135-140	6	3
β-strand	154	1	6
β-strand	156-161	6	3
β-strand	162	1	9
α-helix	165-169	5
β-strand	180-183	4	9
α-helix	186-186B	3
β-strand	189	1	2
β-strand	198-202	5	3
β-strand	207-212	6	3
β-strand	213-215	3	9
β-strand	226-229	4	9
α-helix	235-245	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
thrombin light chain	1	protein	36	Homo sapiens	P00734 (AlphaFold model)
thrombin Heavy chain	2	protein	259	Homo sapiens	P00734 (AlphaFold model)
Hirugen	3	protein	10		P28504 (AlphaFold model)
Inhibitor peptide RPPGF	4	protein	5		P01042 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>1NY2_1 thrombin light chain (chains 1)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (2), FASTA

>1NY2_2 thrombin Heavy chain (chains 2)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (3), FASTA

>1NY2_3 Hirugen (chains 3)
DFEEIPEEYL

Sequence of entity 4 (4), FASTA

>1NY2_4 Inhibitor peptide RPPGF (chains 4)
RPPGF

Primary citation

Mechanisms of Arg-Pro-Pro-Gly-Phe inhibition of thrombin. Hasan, A.A., Warnock, M., Nieman, M. et al. Am J Physiol Heart Circ Physiol (2003) 285:H183-H193. DOI 10.1152/ajpheart.00490.2002 · 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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