6M3B: HAPC-c25k23 Fab complex

hAPC-c25k23 Fab complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,892
Mol. weight: 92.51 kDa
Ligands: NAG
Released: 8 Jul 2020

Explore 6M3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M3B contains 27 α-helices and 78 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
α-helix	19	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	56-59	4
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-90	10	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	123-125	3
α-helix	126-128	3
α-helix	128A-129A	5
β-strand	135-140	6	2
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	235-242	8

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	10
β-strand	5	1	11
β-strand	9-12	4	12
β-strand	18-23	6	11
α-helix	29-31	3
β-strand	36-40	5	12
β-strand	47-50	4	12
β-strand	51	1	13
β-strand	55	1	13
β-strand	64-69	6	11
β-strand	72-77	6	11
α-helix	82-84	3
β-strand	86-94	9	12
β-strand	99-102	4	12
β-strand	103	1	10
β-strand	106-110	5	12
β-strand	116	1	14
α-helix	117-118	2
β-strand	119-123	5	15
α-helix	124-126	3
α-helix	127-131	5
β-strand	135-144	10	15
β-strand	145	1	14
β-strand	150-155	6	16
β-strand	158-159	2	16
β-strand	164-166	3	15
α-helix	167-169	3
β-strand	170-171	2	15
β-strand	177-185	9	15
α-helix	187-191	5
β-strand	196-202	7	16
β-strand	205-211	7	16

Chain C: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-96	5	18
β-strand	100	1	19
β-strand	110	1	19
β-strand	118-122	5	18
β-strand	128	1	20
α-helix	129-130	2
β-strand	131-135	5	21
β-strand	142	1	21
β-strand	146-156	11	21
β-strand	157	1	20
β-strand	162-165	4	22
α-helix	166-168	3
β-strand	174-176	3	21
α-helix	177-179	3
β-strand	180-181	2	21
α-helix	182	1
β-strand	187-196	10	21
β-strand	206	1	23
β-strand	207-211	5	22
α-helix	212-214	3
β-strand	216-217	2	22
β-strand	221	1	23

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	6
β-strand	78-80	3	6
α-helix	81	1
β-strand	84-85	2	7
β-strand	91-92	2	7
α-helix	101-104	4
β-strand	108-111	4	8
β-strand	116-119	4	8
β-strand	124-126	3	9
β-strand	133-135	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K-dependent protein C heavy chain	A	protein	250	Homo sapiens	P04070 (AlphaFold model)
Vitamin K-dependent protein C light chain	D	protein	155	Homo sapiens	P04070 (AlphaFold model)
c25k23 Fab L chain	B	protein	214	Homo sapiens
c25k23 Fab H chain	C	protein	223	Homo sapiens

Sequence of entity 1 (A), FASTA

>6M3B_1 Vitamin K-dependent protein C heavy chain (chains A)
LIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLR
RWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELN
QAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGIL
GDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD
KEAPQKSWAP

Sequence of entity 2 (D), FASTA

>6M3B_2 Vitamin K-dependent protein C light chain (chains D)
ANSFLEELRHSSLERECIEEICDFEEAKEIFQNVDDTLAFWSKHVDGDQCLVLPLEHPCA
SLCCGHGTCIDGIGSFSCDCRSGWEGRFCQREVSFLNCSLDNGGCTHYCLEEVGWRRCSC
APGYKLGDDLLQCHPAVKFPCGRPWKRMEKKRSHL

Sequence of entity 3 (B), FASTA

>6M3B_3 c25k23 Fab L chain (chains B)
SVLTQPPSASGTPGQRVTISCTGSSSNIGAAYDVHWYQQLPGTAPKLLIYGNNKRPSGVP
DRFSGSKSGTSASLAISGLRSEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE

Sequence of entity 4 (C), FASTA

>6M3B_4 c25k23 Fab H chain (chains C)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVSGVSWNGSRTHY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCALTGRSGWMRFPNWFDPWGQGTLV
TVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Targeted inhibition of activated protein C by a non-active-site inhibitory antibody to treat hemophilia. Zhao, X.Y., Wilmen, A., Wang, D. et al. Nat Commun (2020) 11:2992-2992. DOI 10.1038/s41467-020-16720-9 · 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…
1AUT 2.8 Å, Human activated protein C
3F6U 2.8 Å, Crystal structure of human Activated Protein C (APC) complexed with PPACK
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

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