3HKI: Murine thrombin mutant W215A/E217A

Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 5,254
Mol. weight: 75.59 kDa
Ligands: NAG
Released: 7 Jul 2009

Explore 3HKI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HKI contains 31 α-helices and 44 β-strands across 6 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	1C-1A	3
α-helix	8-10	3
α-helix	14C-14I	7

Chain B: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-36	7	3
β-strand	38-46	9	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
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-83	3	3
β-strand	85-90	6	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	5
β-strand	156-162	7	2
α-helix	165-169	5
β-strand	180-183	4	2
β-strand	189	1	1
α-helix	192-194	3
β-strand	198-202	5	2
β-strand	207-215	9	2
α-helix	220-221A	3
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-245	11

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	47-49	3

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	1C-1A	3
α-helix	5-9	5
α-helix	14C-14K	9

Chain E: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	6
β-strand	20-21	2	7
α-helix	22-23	2
β-strand	30-35	6	8
β-strand	39-46	8	8
β-strand	51-54	4	8
α-helix	56-59	4
β-strand	60-60A	2	9
α-helix	60B-60D	3
β-strand	60F-60G	2	9
α-helix	61-63	3
β-strand	64-68	5	8
β-strand	72	1	10
β-strand	81-83	3	8
β-strand	85-90	6	8
β-strand	95	1	11
β-strand	100	1	11
β-strand	104-108	5	8
α-helix	120-121	2
β-strand	122	1	7
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	7
β-strand	154	1	10
β-strand	156-163	8	7
α-helix	165-170	6
β-strand	180-183	4	7
β-strand	189	1	6
α-helix	192-194	3
β-strand	198-202	5	7
β-strand	207-215	9	7
β-strand	226-230	5	7
α-helix	231-245	15

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	52-54	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, D	protein	44	Mus musculus	P19221 (AlphaFold model)
Thrombin heavy chain	B, E	protein	258	Mus musculus	P19221 (AlphaFold model)
Proteinase-activated receptor 1	C, F	protein	21	Homo sapiens	P25116 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3HKI_1 Thrombin light chain (chains A, D)
FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDGR

Sequence of entity 2 (B, E), FASTA

>3HKI_2 Thrombin heavy chain (chains B, E)
IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLL
VRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCL
PDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIR
ITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSAGAGCDRKGKYGFY
THVFRLKRWIQKVIDQFG

Sequence of entity 3 (C, F), FASTA

>3HKI_3 Proteinase-activated receptor 1 (chains C, F)
SFLLRNPNDKYEPFWEDEEKN

Ligands and cofactors

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

Primary citation

Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A. Gandhi, P.S., Page, M.J., Chen, Z. et al. J Biol Chem (2009) 284:24098-24105. DOI 10.1074/jbc.M109.025403 · 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
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…
2PV9 3.5 Å, Crystal structure of murine thrombin in complex with the extracellular fragment of…

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