1NRP: Crystallographic structures of thrombin

Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes. Determined by X-ray diffraction at 3.0 Å resolution. Released 31 May 1994.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,445
Mol. weight: 36.8 kDa
Released: 31 May 1994

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

Secondary structure: helices and β-sheets

1NRP contains 8 α-helices and 26 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: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	52-54	3	3
α-helix	60B-60D	3
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	104-108	5	3
β-strand	115	1	5
β-strand	118	1	5
β-strand	122	1	2
α-helix	126-129B	6
β-strand	132	1	6
β-strand	136-140	5	2
β-strand	154	1	4
β-strand	156-160	5	2
α-helix	161	1
β-strand	162	1	6
α-helix	163	1
α-helix	165-168	4
β-strand	180-182	3	7
β-strand	183	1	6
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-212	6	2
β-strand	213-215	3	7
β-strand	227-229	3	7
α-helix	235-240	6

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14D-14G	4

Chain R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	39	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-thrombin (small subunit)	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Alpha-thrombin (large subunit)	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Receptor based peptide nr's	R	protein	23	Homo sapiens	P25116 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1NRP_1 ALPHA-THROMBIN (SMALL SUBUNIT) (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>1NRP_2 ALPHA-THROMBIN (LARGE SUBUNIT) (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (R), FASTA

>1NRP_3 RECEPTOR BASED PEPTIDE NR'S (chains R)
LDPRSFLLRNPNDKYEPFWEDEE

Primary citation

Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes. Mathews, I.I., Padmanabhan, K.P., Ganesh, V. et al. Biochemistry (1994) 33:3266-3279. DOI 10.1021/bi00177a018 · 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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