2PV9: Murine thrombin

Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4. Determined by X-ray diffraction at 3.5 Å resolution. Released 10 Jul 2007.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Mus musculus
Chains: 3
Atoms: 2,679
Mol. weight: 38.34 kDa
Ligands: NAG
Released: 10 Jul 2007

Explore 2PV9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PV9 contains 10 α-helices and 25 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 A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1C-1A	3
α-helix	14C-14G	5

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	31-35	5	3
β-strand	39-44	6	3
β-strand	45-46	2	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
β-strand	64-68	5	3
β-strand	72	1	6
β-strand	81-84	4	3
β-strand	85-90	6	4
β-strand	95	1	7
β-strand	100	1	7
β-strand	104-108	5	4
α-helix	112-114	3
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	6
β-strand	156-162	7	2
α-helix	165-170	6
β-strand	180-183	4	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	231-244	14

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	57-58	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A	protein	44	Mus musculus	P19221 (AlphaFold model)
Thrombin heavy chain	B	protein	258	Mus musculus	P19221 (AlphaFold model)
Proteinase-activated receptor 4	C	protein	26		O88634 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PV9_1 Thrombin light chain (chains A)
FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDGR

Sequence of entity 2 (B), FASTA

>2PV9_2 Thrombin heavy chain (chains B)
IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLL
VRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCL
PDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIR
ITDNMFCAGFKVNDTKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRKGKYGFY
THVFRLKRWIQKVIDQFG

Sequence of entity 3 (C), FASTA

>2PV9_3 Proteinase-activated receptor 4 (chains C)
KSSDKPNPRGYPGKFCANDSDTLELP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Bah, A., Chen, Z., Bush-Pelc, L.A. et al. Proc Natl Acad Sci U S A (2007) 104:11603-11608. DOI 10.1073/pnas.0704409104 · PubMed

Other PDB entries of the same protein (UniProt P19221 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HK3 1.94 Å, Crystal structure of murine thrombin mutant W215A/E217A (one molecule in the asymmetric…
2PUX 2.0 Å, Crystal structure of murine thrombin in complex with the extracellular fragment of…
2OCV 2.2 Å, Structural basis of Na+ activation mimicry in murine thrombin
3HKI 2.2 Å, Crystal structure of murine thrombin mutant W215A/E217A in complex with the…
3EDX 2.4 Å, Crystal structure of the W215A/E217A mutant of murine thrombin
3HK6 3.2 Å, Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric…

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