2Y5F: Factor xa - cation inhibitor complex

Factor xa - cation inhibitor complex. Determined by X-ray diffraction at 1.29 Å resolution. Released 28 Dec 2011.

Method: X-ray diffraction
Resolution: 1.29 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,782
Mol. weight: 32.89 kDa
Ligands: XWG
Released: 28 Dec 2011

Explore 2Y5F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Y5F contains 12 α-helices and 27 β-strands across 2 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: 11 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	30-34	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	72	1	4
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	104-108	5	3
β-strand	115	1	5
β-strand	118	1	5
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	6
α-helix	150	1
β-strand	151	1	6
α-helix	152	1
β-strand	154	1	4
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	99-102	4	7
β-strand	107-110	4	7
β-strand	115-117	3	8
β-strand	124-126	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated factor xa heavy chain	A	protein	234	HOMO SAPIENS	P00742 (AlphaFold model)
Factor X light chain	L	protein	54	HOMO SAPIENS	P00742 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2Y5F_1 ACTIVATED FACTOR XA HEAVY CHAIN (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGEQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT

Sequence of entity 2 (L), FASTA

>2Y5F_2 FACTOR X LIGHT CHAIN (chains L)
KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERR

Ligands and cofactors

ID	Name	Formula	Copies
XWG	(3AS,4R,5S,8AS,8BR)-4-[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]-2-[3-[1-(2-hy…	C25 H32 Cl N4 O4 S	1

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

Primary citation

Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water. Salonen, L.M., Holland, M.C., Kaib, P.S. et al. Chemistry (2012) 18:213. DOI 10.1002/CHEM.201102571 · PubMed

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

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
2JKH 1.25 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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