3F6U: Human Activated Protein C

Crystal structure of human Activated Protein C (APC) complexed with PPACK. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,818
Mol. weight: 38.29 kDa
Ligands: 0G6, CA
Released: 25 Nov 2008

Explore 3F6U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F6U contains 13 α-helices and 30 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 H: 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	40-48	9	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	95	1	5
β-strand	100	1	5
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	6
β-strand	118	1	6
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
α-helix	126-128	3
α-helix	128A-129A	5
β-strand	135-140	6	2
β-strand	154	1	4
α-helix	155	1
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	231-233	3
α-helix	235-242	8

Chain L: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	7
β-strand	78-80	3	7
α-helix	81	1
β-strand	84-85	2	8
β-strand	91-92	2	8
α-helix	101-104	4
β-strand	108-111	4	9
β-strand	116-119	4	9
β-strand	124-126	3	10
β-strand	133-135	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K-dependent protein C heavy chain	H	protein	240	Homo sapiens	P04070 (AlphaFold model)
Vitamin K-dependent protein C light chain	L	protein	98	Homo sapiens	P04070 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>3F6U_1 Vitamin K-dependent protein C heavy chain (chains H)
LIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLR
RWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELN
QAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGIL
GDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD

Sequence of entity 2 (L), FASTA

>3F6U_2 Vitamin K-dependent protein C light chain (chains L)
QCLVLPLEHPCASLCCGHGTCIDGIGSFSCDCRSGWEGRFCQREVSFLNCSLDNGGCTHY
CLEEVGWRRCSCAPGYKLGDDLLQCHPAVKFPCGRPWK

Ligands and cofactors

ID	Name	Formula	Copies
0G6	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexa…	C21 H34 Cl N6 O3	1
CA	Calcium ion	Ca	1

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

Primary citation

Thermodynamic linkage between the S1 site, the Na+ site, and the Ca2+ site in the protease domain of human activated protein C (APC). Schmidt, A.E., Padmanabhan, K., Underwood, M.C. et al. J Biol Chem (2002) 277:28987-28995. DOI 10.1074/jbc.M201892200 · PubMed

Other PDB entries of the same protein (UniProt P04070 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LQV 1.6 Å, Crystal structure of the Endothelial protein C receptor with phospholipid in the groove…
3JTC 1.6 Å, Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid…
4DT7 1.9 Å, Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of…
6M3B 2.2 Å, hAPC-c25k23 Fab complex
1AUT 2.8 Å, Human activated protein C
9MOV 3.0 Å, Cryo-EM structure of factor Va bound to activated protein C
9MOT 3.15 Å, Cryo-EM structure of factor Va bound to activated protein C
8JRV 3.3 Å, Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1
9BVM 3.4 Å, Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich…
8JRU 3.5 Å, Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state
6M3C 3.7 Å, hAPC-h1573 Fab complex

Browse structure collections

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