3EDX: W215A/E217A mutant of murine thrombin

Crystal structure of the W215A/E217A mutant of murine thrombin. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Mus musculus
Chains: 6
Atoms: 7,612
Mol. weight: 106.04 kDa
Ligands: NAG
Released: 7 Jul 2009

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

Secondary structure: helices and β-sheets

3EDX contains 48 α-helices and 64 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.

Chains A, C and E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	8-10	3
α-helix	14C-14G	5

Chain B: 13 helices, 23 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	56-59	4
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	81-90	10	3
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	6
β-strand	118	1	6
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
α-helix	149C-149E	3
β-strand	154	1	5
β-strand	156-163	8	2
α-helix	164	1
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
β-strand	221A	1	7
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-244	10

Chain D: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	8
β-strand	20-21	2	9
α-helix	22-23	2
β-strand	30-35	6	10
β-strand	39-46	8	10
β-strand	51-54	4	10
α-helix	56-58	3
β-strand	60-60A	2	11
α-helix	60B-60D	3
β-strand	60F-60G	2	11
β-strand	64-68	5	10
β-strand	72	1	12
β-strand	81-90	10	10
β-strand	104-108	5	10
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	9
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	9
α-helix	149C-150	4
β-strand	154	1	12
β-strand	156-162	7	9
α-helix	163-164	2
α-helix	165-169	5
β-strand	180-183	4	9
β-strand	189	1	8
α-helix	192-194	3
β-strand	198-202	5	9
β-strand	207-215	9	9
β-strand	226-230	5	9
α-helix	232-234	3
α-helix	235-244	10

Chain F: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	13
β-strand	20-21	2	14
α-helix	22-23	2
β-strand	30-35	6	15
β-strand	39-46	8	15
β-strand	51-54	4	15
α-helix	56-59	4
β-strand	60-60A	2	16
α-helix	60B-60D	3
β-strand	60F-60G	2	16
β-strand	64-68	5	15
β-strand	72	1	17
β-strand	81-90	10	15
β-strand	104-108	5	15
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	14
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	14
α-helix	149C-150	4
β-strand	154	1	17
β-strand	156-162	7	14
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	14
β-strand	189	1	13
α-helix	192-194	3
β-strand	198-202	5	14
β-strand	207-215	9	14
β-strand	221A	1	7
β-strand	226-230	5	14
α-helix	231-234	4
α-helix	235-244	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, C, E	protein	44	Mus musculus	P19221 (AlphaFold model)
Thrombin heavy chain	B, D, F	protein	258	Mus musculus	P19221 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>3EDX_1 Thrombin light chain (chains A, C, E)
FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDGR

Sequence of entity 2 (B, D, F), FASTA

>3EDX_2 Thrombin heavy chain (chains B, D, F)
IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLL
VRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCL
PDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIR
ITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSAGAGCDRKGKYGFY
THVFRLKRWIQKVIDQFG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular Basis for the Kinetic Differences of the W215A/E217A Mutant of Human and Murine Thrombin. Gandhi, P.S., Page, M.J., Chen, Z. et al. To be published.

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…
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…

Browse structure collections

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