2WPJ: Coagulation factor ixa light chain

factor IXa superactive triple mutant, NaCl-soaked. Determined by X-ray diffraction at 1.6 Å resolution. Released 22 Dec 2009.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 3
Atoms: 2,684
Mol. weight: 33.04 kDa
Ligands: CA
Released: 22 Dec 2009

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

Secondary structure: helices and β-sheets

2WPJ contains 10 α-helices and 27 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 E: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	91-94	4
β-strand	98-100	3	1
β-strand	108-110	3	1
β-strand	115-117	3	2
β-strand	124-126	3	2

Chain L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	3

Chain S: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	4
β-strand	20-21	2	3
α-helix	22-23	2
β-strand	30-34	5	5
β-strand	42-48	7	5
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	64-66	4	5
β-strand	72	1	6
β-strand	81-90	10	5
β-strand	104-108	5	5
β-strand	115	1	7
β-strand	118	1	7
α-helix	120-121	2
β-strand	122	1	3
α-helix	126-131	8
β-strand	135-140	6	3
β-strand	143	1	8
α-helix	150	1
β-strand	151	1	8
α-helix	152	1
β-strand	154	1	6
β-strand	156-163	8	3
α-helix	165-170	6
β-strand	180-183	4	3
β-strand	189	1	4
β-strand	198-203	6	3
β-strand	206-215	10	3
β-strand	226-230	5	3
α-helix	231-233	3
α-helix	235-241	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor ixa light chain	E	protein	59	HOMO SAPIENS	P00740 (AlphaFold model)
D-phe-pro-arg-chloromethyl ketone	L	protein	3	SYNTHETIC CONSTRUCT
Coagulation factor ixa heavy chain	S	protein	235	HOMO SAPIENS	P00740 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>2WPJ_1 COAGULATION FACTOR IXA LIGHT CHAIN (chains E)
TCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTR

Sequence of entity 2 (L), FASTA

>2WPJ_2 D-PHE-PRO-ARG-CHLOROMETHYL KETONE (chains L)
FPR

Sequence of entity 3 (S), FASTA

>2WPJ_3 COAGULATION FACTOR IXA HEAVY CHAIN (chains S)
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEE
TEHTEQKRNVIRIIPHHNFNAAINTYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFL
KFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTITNNMFCAGFHEGGRDS
CQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural Basis of the Cofactor- and Substrate-Assisted Activation of Human Coagulation Factor Ixa. Zogg, T., Brandstetter, H. Structure (2009) 17:1669. DOI 10.1016/J.STR.2009.10.011 · PubMed

Other PDB entries of the same protein (UniProt P00740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JB9 1.3 Å, Crystal structure of factor IXa K98T variant in complex with PPACK
6MV4 1.37 Å, Crystal structure of human coagulation factor ixa
5JBA 1.4 Å, Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK
5TNT 1.4 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
4YZU 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
4Z0K 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
5JB8 1.45 Å, Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
1EDM 1.5 Å, Epidermal growth factor-like domain from human factor IX
2WPH 1.5 Å, factor IXa superactive triple mutant
5TNO 1.54 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
5JBB 1.56 Å, Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with…
6RFK 1.6 Å, Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

Browse structure collections

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