6M3C: HAPC-h1573 Fab complex

hAPC-h1573 Fab complex. Determined by X-ray diffraction at 3.7 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 12
Atoms: 16,911
Mol. weight: 279.68 kDa
Released: 8 Jul 2020

Explore 6M3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M3C contains 67 α-helices and 215 β-strands across 12 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.

Chains A and C: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	213	1	1
α-helix	215	1
β-strand	216-217	2	2
α-helix	218	1
β-strand	226-230	5	3
β-strand	236-244	9	3
β-strand	247-250	4	3
α-helix	252-254	3
β-strand	262-265	4	3
β-strand	269	1	4
β-strand	278-280	3	3
β-strand	282-287	6	3
β-strand	292	1	5
β-strand	297	1	5
β-strand	301-305	5	3
α-helix	308-311	4
β-strand	312	1	6
β-strand	315	1	6
α-helix	317-318	2
β-strand	319	1	2
α-helix	320-322	3
α-helix	323-325	3
α-helix	326-330	5
β-strand	336-341	6	2
α-helix	350-352	3
β-strand	359	1	4
β-strand	361-368	8	2
α-helix	369	1
α-helix	370-376	7
β-strand	385-388	4	2
β-strand	396	1	1
β-strand	405-410	6	2
β-strand	413-423	11	2
β-strand	433-437	5	2
α-helix	438-440	3
α-helix	442-448	7

Chains B, D and I: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	143-146	4
β-strand	150-153	4	7
β-strand	158-161	4	7
β-strand	166-168	3	8
β-strand	175-177	3	8

Chain E: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	29
β-strand	19-25	7	28
β-strand	37-42	6	29
α-helix	47-48	2
β-strand	49-53	5	29
β-strand	57-58	2	29
α-helix	59	1
β-strand	66-71	6	28
β-strand	74-79	6	28
α-helix	84-86	3
β-strand	88-94	7	29
β-strand	102	1	29
β-strand	106-110	5	29
β-strand	115	1	30
β-strand	118-121	4	31
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	31
β-strand	144	1	30
β-strand	151-154	4	32
β-strand	158	1	32
β-strand	163-164	2	31
α-helix	169-171	3
β-strand	177-186	10	31
α-helix	187-190	4
β-strand	195-199	5	32
β-strand	210-214	5	32

Chain F: 1 helix, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	33
β-strand	11	1	34
β-strand	19-25	7	33
β-strand	33-39	7	35
β-strand	45-51	7	35
β-strand	60	1	35
β-strand	71	1	33
β-strand	74-75	2	33
β-strand	80-84	5	33
β-strand	94-101	8	35
β-strand	108	1	35
β-strand	112-114	3	35
β-strand	115	1	34
β-strand	122	1	36
β-strand	125-129	5	37
β-strand	140-150	11	37
β-strand	151	1	36
β-strand	156-159	4	38
β-strand	168-170	3	37
α-helix	171-173	3
β-strand	174-175	2	37
β-strand	181-190	10	37
β-strand	200-205	6	38
β-strand	210-215	6	38

Chain G: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	213	1	39
α-helix	215	1
β-strand	216-217	2	40
α-helix	218	1
β-strand	226-230	5	41
β-strand	236-244	9	41
β-strand	247-250	4	41
α-helix	252-255	4
β-strand	262-265	4	41
β-strand	269	1	42
β-strand	278-280	3	41
β-strand	282-287	6	41
β-strand	292	1	43
β-strand	297	1	43
β-strand	301-305	5	41
α-helix	308-311	4
β-strand	312	1	44
β-strand	315	1	44
α-helix	317-318	2
β-strand	319	1	40
α-helix	320-322	3
α-helix	323-325	3
α-helix	326-330	5
β-strand	336-341	6	40
α-helix	350-352	3
β-strand	359	1	42
β-strand	361-368	8	40
α-helix	369	1
α-helix	370-376	7
β-strand	385-388	4	40
β-strand	396	1	39
β-strand	405-410	6	40
β-strand	413-422	10	40
β-strand	433-437	5	40
α-helix	438-440	3
α-helix	442-448	7

Chain H: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	14
β-strand	11	1	15
β-strand	19-25	7	14
β-strand	33-39	7	16
β-strand	45-51	7	16
β-strand	60	1	16
β-strand	71	1	14
β-strand	74-75	2	14
β-strand	80-84	5	14
β-strand	94-101	8	16
β-strand	108	1	16
β-strand	112-114	3	16
β-strand	115	1	15
β-strand	122	1	17
β-strand	125-129	5	18
β-strand	140-150	11	18
β-strand	151	1	17
β-strand	156-159	4	19
β-strand	168-170	3	18
α-helix	171-173	3
β-strand	174-175	2	18
β-strand	181-190	10	18
α-helix	191-193	3
β-strand	200-205	6	19
β-strand	210-215	6	19

Chain J: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	47
β-strand	10-13	4	48
β-strand	19-25	7	47
β-strand	37-42	6	48
α-helix	47-48	2
β-strand	49-53	5	48
β-strand	57-58	2	48
α-helix	59	1
β-strand	66-71	6	47
β-strand	74-79	6	47
α-helix	84-86	3
β-strand	88-94	7	48
β-strand	102	1	48
β-strand	106-110	5	48
β-strand	115	1	49
β-strand	118-121	4	50
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	50
β-strand	144	1	49
β-strand	149-154	6	51
β-strand	157-158	2	51
β-strand	163-164	2	50
α-helix	169-171	3
β-strand	177-186	10	50
α-helix	187-190	4
β-strand	195-201	7	51
β-strand	210-214	5	51

Chain K: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	52
β-strand	11	1	53
β-strand	19-21	3	54
β-strand	25	1	52
β-strand	33-39	7	55
β-strand	45-51	7	55
β-strand	60	1	55
β-strand	71	1	54
β-strand	74-75	2	56
β-strand	80-81	2	56
β-strand	82-84	3	54
β-strand	94-101	8	55
β-strand	108	1	55
β-strand	112-114	3	55
β-strand	115	1	53
β-strand	122	1	57
β-strand	125-129	5	58
β-strand	140-150	11	58
β-strand	151	1	57
β-strand	156-159	4	59
β-strand	168-170	3	58
α-helix	171-173	3
β-strand	174-175	2	58
β-strand	181-190	10	58
β-strand	200-205	6	59
β-strand	210-215	6	59

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K-dependent protein C heavy chain	A, C, G	protein	250	Homo sapiens	P04070 (AlphaFold model)
Vitamin K-dependent protein C light chain	B, D, I	protein	155	Homo sapiens	P04070 (AlphaFold model)
h1573 Fab H chain	E, J, L	protein	218	Homo sapiens
h1573 Fab L chain	F, H, K	protein	221	Homo sapiens

Sequence of entity 1 (A, C, G), FASTA

>6M3C_1 Vitamin K-dependent protein C heavy chain (chains A, C, G)
LIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLR
RWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELN
QAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGIL
GDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD
KEAPQKSWAP

Sequence of entity 2 (B, D, I), FASTA

>6M3C_2 Vitamin K-dependent protein C light chain (chains B, D, I)
ANSFLEELRHSSLERECIEEICDFEEAKEIFQNVDDTLAFWSKHVDGDQCLVLPLEHPCA
SLCCGHGTCIDGIGSFSCDCRSGWEGRFCQREVSFLNCSLDNGGCTHYCLEEVGWRRCSC
APGYKLGDDLLQCHPAVKFPCGRPWKRMEKKRSHL

Sequence of entity 3 (E, J, L), FASTA

>6M3C_3 h1573 Fab H chain (chains E, J, L)
DIVLTQSPASLAVSPGQRATITCKASESVDSFGATFMHWYQQKPGQPPKLLIYLASNLES
GVPARFSGSGSGTDFTLTINPVEADDTANYYCQQNNEDPYTFGQGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (F, H, K), FASTA

>6M3C_4 h1573 Fab L chain (chains F, H, K)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSNYYLNWVRQAPGKGLEWVGDIRLKSNNYEK
HYAESVKGRFTISRDDSKNSLYLQMNSLKTEDTAVYYCAREGDYFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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…
6M3B 2.2 Å, hAPC-c25k23 Fab complex
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

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