8EPH: Coagulation factor IXa light chain

Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA. Determined by X-ray diffraction at 1.88 Å resolution. Released 3 Jul 2024.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,564
Mol. weight: 75.47 kDa
Ligands: FUC, CA
Released: 3 Jul 2024

Explore 8EPH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EPH contains 30 α-helices and 60 β-strands across 4 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	50-53	4
α-helix	60	1
β-strand	61-65	5	1
β-strand	68-72	5	1
α-helix	73-74	2
β-strand	77-78	2	2
β-strand	84-85	2	2
α-helix	86	1
α-helix	91-94	4
β-strand	98-101	4	3
α-helix	102	1
β-strand	107-110	4	3
β-strand	115-117	3	4
β-strand	124-126	3	4

Chains B and D: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	5
β-strand	20-21	2	6
α-helix	22-23	2
β-strand	30-34	5	7
β-strand	42-48	7	7
β-strand	51-54	4	7
α-helix	56-58	3
β-strand	65-68	4	7
β-strand	72	1	8
β-strand	81-90	10	7
β-strand	104-108	5	7
β-strand	115	1	9
β-strand	118	1	9
α-helix	120-121	2
β-strand	122	1	6
α-helix	126-132	9
β-strand	135-140	6	6
β-strand	143	1	10
α-helix	150	1
β-strand	151	1	10
α-helix	152	1
β-strand	154	1	8
β-strand	156-163	8	6
α-helix	165-170	6
β-strand	180-183	4	6
β-strand	189	1	5
β-strand	198-203	6	6
β-strand	206-216	11	6
β-strand	226-230	5	6
α-helix	231-234	4
α-helix	235-242	8

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	50-53	4
α-helix	60	1
β-strand	61-65	5	11
β-strand	68-72	5	11
α-helix	73-74	2
β-strand	77-78	2	12
β-strand	84-85	2	12
α-helix	86	1
α-helix	91-94	4
β-strand	98-101	4	13
α-helix	103-105	3
β-strand	107-110	4	13
β-strand	115-117	3	14
β-strand	124-126	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor IXa light chain	A, C	protein	102	Homo sapiens	P00740 (AlphaFold model)
Coagulation factor IXa heavy chain	B, D	protein	235	Homo sapiens	P00740 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8EPH_1 Coagulation factor IXa light chain (chains A, C)
DGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELDVTCNIKNGRCEQFCKNSADNK
VVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTRRKR

Sequence of entity 2 (B, D), FASTA

>8EPH_2 Coagulation factor IXa heavy chain (chains B, D)
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEE
TEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFL
KFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDS
CQGDAGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

Ligands and cofactors

ID	Name	Formula	Copies
FUC	alpha-L-fucopyranose	C6 H12 O5	2
CA	Calcium ion	Ca	4

Primary citation

An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa. Kolyadko, V.N., Layzer, J.M., Perry, K. et al. Proc Natl Acad Sci U S A (2024) 121:e2401136121-e2401136121. DOI 10.1073/pnas.2401136121 · 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…
2WPJ 1.6 Å, factor IXa superactive triple mutant, NaCl-soaked

Browse structure collections

About this viewer

MolViewer shows 8EPH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.