9I24: Activated factor Xa heavy chain

Coagulation factor Xa complex with a2-loop peptide. Determined by X-ray diffraction at 1.2 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 1.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 2,754
Mol. weight: 37.37 kDa
Ligands: 0GJ, CA
Released: 26 Nov 2025

Explore 9I24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I24 contains 10 α-helices and 26 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 C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	16-19	4	3

Chain H: 9 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	30-34	5	3
β-strand	40-46	7	3
β-strand	51-54	4	3
α-helix	56-60	5
β-strand	65-68	4	3
β-strand	81-83	3	3
β-strand	85-91	7	3
β-strand	104-108	5	3
β-strand	115	1	4
β-strand	118	1	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-124A	3
α-helix	125-127	3
α-helix	128-131A	5
β-strand	135-140	6	2
β-strand	143	1	5
β-strand	151	1	5
β-strand	156-163	8	2
α-helix	165-171	7
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-241	7

Chain L: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	92-95	4
β-strand	99-103	5	6
β-strand	106-110	5	6
β-strand	115-117	3	7
β-strand	124-126	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated factor Xa heavy chain	H	protein	254	Homo sapiens	P00742 (AlphaFold model)
Factor X light chain	L	protein	55	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor V heavy chain	C	protein	15	synthetic construct	P12259 (AlphaFold model)
GLU-GLY-ARG-chloromethyl ketone inhibitor (EGRCK)	I	protein	3	synthetic construct

Sequence of entity 1 (H), FASTA

>9I24_1 Activated factor Xa heavy chain (chains H)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTKTRGLP
KAKSHAPEVITSSP

Sequence of entity 2 (L), FASTA

>9I24_2 Factor X light chain (chains L)
MRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLER

Sequence of entity 3 (C), FASTA

>9I24_3 Coagulation factor V heavy chain (chains C)
CIPDDDEDSYEIFEP

Sequence of entity 4 (I), FASTA

>9I24_4 GLU-GLY-ARG-chloromethyl ketone inhibitor (EGRCK) (chains I)
EGR

Ligands and cofactors

ID	Name	Formula	Copies
0GJ	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydr…	C14 H28 Cl N6 O5	1
CA	Calcium ion	Ca	1

Water and common crystallization additives (IMD, CL, NA) are not listed.

Primary citation

A 3.3- angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex. Ustok, F.I., Faille, A., Huntington, J.A. Blood (2026) 147:573-583. DOI 10.1182/blood.2025031527 · PubMed

Other PDB entries of the same protein (UniProt P00742 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2JKH 1.25 Å, Factor Xa - cation inhibitor complex
2Y5F 1.29 Å, Factor xa - cation inhibitor complex
2Y5G 1.29 Å, Factor xa - cation inhibitor complex
2Y5H 1.33 Å, Factor xa - cation inhibitor complex
3KL6 1.45 Å, Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and…
2PR3 1.5 Å, Factor XA inhibitor
6YYX 1.53 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
3FFG 1.54 Å, Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPH…
7YB9 1.54 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
4Y6D 1.55 Å, Factor Xa complex with GTC000101
2VWO 1.6 Å, Aminopyrrolidine Factor Xa inhibitor
3CEN 1.6 Å, Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl)…

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