4Y6D: Factor Xa complex with GTC000101

Factor Xa complex with GTC000101. Determined by X-ray diffraction at 1.55 Å resolution. Released 30 Sept 2015.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,623
Mol. weight: 44.23 kDa
Ligands: 48U
Released: 30 Sept 2015

Explore 4Y6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y6D contains 13 α-helices and 26 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, 22 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	82-90	9	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	123-124	3
α-helix	125-127	3
α-helix	128-131B	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	156-162	7	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 B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
α-helix	4-7	4
β-strand	11-15	5	7
β-strand	18-22	5	7
β-strand	27-29	3	8
β-strand	36-38	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor X	A	protein	254	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor X	B	protein	134	Homo sapiens	P00742 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4Y6D_1 Coagulation factor X (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKA
KSHAPEVITSSPLK

Sequence of entity 2 (B), FASTA

>4Y6D_2 Coagulation factor X (chains B)
EEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGL
GEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACI
PTGPYPCGKQTLER

Ligands and cofactors

ID	Name	Formula	Copies
48U	4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxopyrrolid…	C19 H19 Cl F N3 O4 S2	1

Primary citation

TBA. Convery, M.A. To be published.

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
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…
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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