5B71: Complement C5

Crystal structure of complement C5 in complex with SKY59. Determined by X-ray diffraction at 2.11 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,217
Mol. weight: 119.5 kDa
Released: 3 May 2017

Explore 5B71 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B71 contains 31 α-helices and 107 β-strands across 6 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-65	4	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	100	1
β-strand	101	1	2
α-helix	102	1
β-strand	105-109	5	2
β-strand	114	1	3
α-helix	115-116	2
β-strand	117-121	5	4
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	4
β-strand	143	1	3
β-strand	147-153	7	5
β-strand	156-157	2	5
α-helix	158	1
β-strand	162-166	5	4
α-helix	167-170	4
β-strand	176-185	10	4
α-helix	186-191	6
β-strand	194-201	8	5
β-strand	208-213	6	5
α-helix	214-216	3

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
α-helix	16-17	2
β-strand	18-25	8	6
β-strand	34-40	7	7
β-strand	46-53	8	7
β-strand	59-61	3	7
β-strand	69-73	5	6
β-strand	79-84	6	6
α-helix	89-91	3
β-strand	93-99	7	7
α-helix	102-104	3
β-strand	112-113	2	7
β-strand	117-121	5	7
α-helix	124-126	3
β-strand	127	1	8
α-helix	128-129	2
β-strand	130-134	5	9
β-strand	145-155	11	9
β-strand	156	1	8
β-strand	161-164	4	10
β-strand	169	1	10
β-strand	173-175	3	9
α-helix	176-178	3
β-strand	179-180	2	9
β-strand	186-195	10	9
α-helix	196-200	5
β-strand	205-210	6	10
β-strand	215-220	6	10

Chain C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-48	4	12
β-strand	49	1	13
β-strand	53	1	13
β-strand	62-66	5	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
α-helix	100	1
β-strand	101	1	12
α-helix	102	1
β-strand	105-109	5	12
β-strand	114	1	14
α-helix	115-116	2
β-strand	117-121	5	15
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	15
β-strand	143	1	14
β-strand	147-153	7	16
β-strand	156-157	2	16
β-strand	162-166	5	15
α-helix	167-170	4
β-strand	176-185	10	15
α-helix	186-190	5
β-strand	194-201	8	16
β-strand	208-213	6	16

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
β-strand	34-40	7	18
β-strand	46-53	8	18
β-strand	59-61	3	18
β-strand	69-74	6	17
β-strand	79-84	6	17
α-helix	89-91	3
β-strand	93-99	7	18
β-strand	112-113	2	18
β-strand	117-121	5	18
α-helix	124-126	3
β-strand	127	1	19
α-helix	128-129	2
β-strand	130-134	5	20
β-strand	146-155	10	20
β-strand	156	1	19
β-strand	161-164	4	21
β-strand	169	1	21
β-strand	173-175	3	20
α-helix	176-178	3
β-strand	179-180	2	20
β-strand	186-194	9	20
α-helix	196-200	5
β-strand	204-210	7	21
β-strand	215-221	7	21

Chain E: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	22
β-strand	31-32	2	23
β-strand	33	1	24
β-strand	36-44	9	22
β-strand	50-58	9	25
β-strand	65-73	9	25
β-strand	80-86	7	22
β-strand	87	1	24
β-strand	101-107	7	25
β-strand	112-118	7	25
β-strand	119-120	2	23

Chain F: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	26
β-strand	31-32	2	27
β-strand	37-44	8	26
β-strand	50-58	9	28
β-strand	65-73	9	28
β-strand	80-85	6	26
β-strand	102-107	6	28
β-strand	112-117	6	28
β-strand	119-120	2	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SKY59 Fab light chain	A, C	protein	217	Homo sapiens
SKY59 Fab heavy chain	B, D	protein	228	Homo sapiens
Complement C5 beta chain	E, F	protein	110	Homo sapiens	P01031 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5B71_1 SKY59 Fab light chain (chains A, C)
DIQMTQSPSSLSASVGDRVTITCRASQGISSSLAWYQQKPGKAPKLLIYGASETESGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQNTKVGSSYGNTFGGGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>5B71_2 SKY59 Fab heavy chain (chains B, D)
QVQLVESGGGLVQPGRSLRLSCAASGFTVHSSYYMAWVRQAPGKGLEWVGAIFTGSGAEY
KAEWAKGRVTISKDTSKNQVVLTMTNMDPVDTATYYCASDAGYDYPTHAMHYWGQGTLVT
VSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPP

Sequence of entity 3 (E, F), FASTA

>5B71_3 Complement C5 beta chain (chains E, F)
GSPEFEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLS
SENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNG

Primary citation

Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases. Fukuzawa, T., Sampei, Z., Haraya, K. et al. Sci Rep (2017) 7:1080-1080. DOI 10.1038/s41598-017-01087-7 · PubMed

Other PDB entries of the same protein (UniProt P01031 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Y6C 2.0 Å, X-ray structure analysis of human Complement Component 5 TE domain in complex with the…
4UU9 2.12 Å, Crystal structure of the human c5a in complex with MEDI7814 a neutralising antibody
7AD7 2.3 Å, Crystal structure of human complement C5 in complex with the K8 bovine knob domain…
5B4P 2.4 Å, Complex structure of human C5a and its binding repebody
4P39 2.4 Å, Crystal structure of the human C5aR antagonist C5a-A8
7OP0 2.57 Å, Crystal structure of complement C5 in complex with chemically synthesized K92 knob domain.
3HQA 2.59 Å, Crystal structure of human desarg-C5A
5HCC 2.59 Å, Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Dermacentor…
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
6RPT 2.7 Å, Structure of tick complement inhibitor CirpT1 complexed with macroglobubulin domain 4 of…
7AD6 2.75 Å, Crystal structure of human complement C5 in complex with the K92 bovine knob domain…
22GK 2.84 Å, C5a bound C5aR2 in complex with beta-arrestin1

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