7AD7: Human complement C5

Crystal structure of human complement C5 in complex with the K8 bovine knob domain peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Mar 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 12,100
Mol. weight: 384.31 kDa
Ligands: TAM, CYS, MHA, EOH
Released: 10 Mar 2021

Explore 7AD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AD7 contains 47 α-helices and 111 β-strands across 3 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: 29 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	684-689	6
α-helix	696-703	8
α-helix	711-715	5
α-helix	722-738	17
β-strand	764-765	2	7
α-helix	770-772	3
β-strand	773	1	16
β-strand	777-780	4	16
β-strand	783-789	7	14
α-helix	790-791	2
β-strand	796-805	10	16
β-strand	808-811	4	16
α-helix	812-814	3
β-strand	815-818	4	16
β-strand	819	1	15
β-strand	823-828	6	17
β-strand	833-834	2	18
β-strand	838-847	10	17
β-strand	853-855	3	19
β-strand	856-859	4	18
α-helix	860-862	3
β-strand	865-866	2	20
β-strand	886-888	3	19
β-strand	892-900	9	17
β-strand	901-902	2	20
β-strand	906-915	10	18
β-strand	920-930	11	18
β-strand	934-944	11	21
β-strand	945	1	22
β-strand	954	1	22
β-strand	956-959	4	23
β-strand	967	1	21
α-helix	968	1
β-strand	974-980	7	21
α-helix	985-992	8
α-helix	1008-1013	6
α-helix	1016-1027	12
α-helix	1031-1033	3
α-helix	1038-1054	17
α-helix	1057-1059	3
β-strand	1060	1	24
β-strand	1066	1	24
β-strand	1067	1	25
β-strand	1074	1	25
α-helix	1076-1089	14
α-helix	1097-1110	14
β-strand	1112	1	26
β-strand	1118	1	26
α-helix	1133-1156	24
α-helix	1162-1178	17
α-helix	1185-1196	12
α-helix	1203-1214	12
β-strand	1217-1219	3	27
β-strand	1225-1227	3	27
α-helix	1245-1260	16
α-helix	1264-1277	14
α-helix	1287-1303	17
α-helix	1305-1308	4
β-strand	1310-1317	8	23
β-strand	1322-1329	8	23
β-strand	1332	1	23
β-strand	1334	1	21
β-strand	1338-1340	3	21
β-strand	1346-1350	5	23
β-strand	1354	1	23
β-strand	1357-1367	11	21
β-strand	1377-1386	10	28
β-strand	1399-1408	10	28
α-helix	1410-1411	2
β-strand	1422-1427	6	29
α-helix	1428-1429	2
β-strand	1432-1434	3	28
α-helix	1436-1444	9
β-strand	1452-1456	5	29
β-strand	1459-1464	6	29
β-strand	1473-1481	9	28
β-strand	1485-1486	2	17
α-helix	1488-1490	3
β-strand	1491-1497	7	29
β-strand	1500-1509	10	29

Chain B: 16 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	31-32	2	2
β-strand	37-44	8	1
β-strand	50-58	9	3
β-strand	65-73	9	3
β-strand	80-85	6	1
α-helix	89-91	3
β-strand	101-108	8	3
β-strand	112-118	7	3
β-strand	119-120	2	2
β-strand	125-130	6	4
β-strand	134-135	2	5
β-strand	140-141	2	6
β-strand	143-148	6	4
β-strand	154	1	4
β-strand	159-164	6	5
β-strand	170-176	7	5
β-strand	182-184	3	4
β-strand	188-189	2	6
α-helix	190-191	2
β-strand	197-205	9	5
β-strand	212-219	8	5
β-strand	221-222	2	7
β-strand	228-233	6	8
β-strand	237-238	2	8
β-strand	246-253	8	8
β-strand	259	1	8
α-helix	260	1
β-strand	262-272	11	8
β-strand	289-293	5	8
β-strand	296-301	6	8
α-helix	303-306	4
α-helix	315-318	4
β-strand	322-331	10	8
β-strand	337-347	11	8
β-strand	353-356	4	9
β-strand	362-363	2	10
α-helix	368	1
β-strand	369-376	8	9
β-strand	382	1	9
β-strand	387-396	10	10
β-strand	401-403	3	10
α-helix	404-406	3
β-strand	407-410	4	10
β-strand	417-422	6	9
β-strand	428-437	10	10
α-helix	444-446	3
β-strand	449-456	8	10
β-strand	464-468	5	11
α-helix	475	1
β-strand	476	1	12
α-helix	477	1
β-strand	481-489	9	11
α-helix	493-495	3
β-strand	498-505	8	13
β-strand	508-516	9	13
α-helix	517-518	2
β-strand	524-529	6	11
α-helix	532-534	3
β-strand	537-547	11	13
β-strand	552-562	11	13
β-strand	563	1	12
β-strand	571-576	6	14
β-strand	582	1	15
β-strand	587-594	8	14
β-strand	598-606	9	16
α-helix	607-610	4
α-helix	628-630	3
β-strand	637	1	13
α-helix	642-648	7
β-strand	651-655	5	1

Chain C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	30
α-helix	3-4	2
β-strand	7-16	10	28
β-strand	21-30	10	28
β-strand	40-42	3	28
α-helix	44-46	3
β-strand	47	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C5	A, B	protein	1676	Homo sapiens	P01031 (AlphaFold model)
K8 peptide	C	protein	52	Bos taurus

Sequence of entity 1 (A, B), FASTA

>7AD7_1 Complement C5 (chains A, B)
MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYP
DKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPIT
YDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHI
GIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGY
KNFKNFEITIKARYFYNKVVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVT
FDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATP
LFLKPGIPYPIKVQVKDSLDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASF
VLNLPSGVTVLEFNVKTDAPDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGE
HLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRL
LVYYIVTGEQTAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWV
ALAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANAD
DSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISL
GPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLV
PRRKQLQFALPDSLTTWEIQGVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQ
LKGTVYNYRTSGMQFCVKMSAVEGICTSESPVIDHQGTKSSKCVRQKVEGSSSHLVTFTV
LPLEIGLHNINFSLETWFGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFP
YRIPLDLVPKTEIKRILSVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFY
VFHYLETGNHWNIFHSDPLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTA
FALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEAREN
SLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDK
THPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLN
LKDINYVNPVIKWLSEEQRYGGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHK
GALHNYKMTDKNFLGRPVEVLLNDDLIVSTGFGSGLATVHVTTVVHKTSTSEEVCSFYLK
IDTQDIEASHYRGYGNSDYKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLK
ALVEGVDQLFTDYQIKDGHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHR
PDKQCTMFYSTSNIKIQKVCEGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYA
YKVSITSITVENVFVKYKATLLDIYKTGEAVAEKDSEITFIKKVTCTNAELVKGRQYLIM
GKEALQIKYNFSFRYIYPLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGC

Sequence of entity 2 (C), FASTA

>7AD7_2 K8 peptide (chains C)
SVCPDGFDWGYGCAAGSSRFCTRHDWCCYDERADSHTYGFCTGNRVENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	1
CYS	Cysteine	C3 H7 N O2 S	1
MHA	(carbamoylmethyl-carboxymethyl-amino)-acetic acid	C6 H10 N2 O5	1
EOH	Ethanol	C2 H6 O	4

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

Primary citation

The allosteric modulation of Complement C5 by knob domain peptides. Macpherson, A., Laabei, M., Ahdash, Z. et al. Elife (2021) 10. DOI 10.7554/eLife.63586 · 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…
5B71 2.11 Å, Crystal structure of complement C5 in complex with SKY59
4UU9 2.12 Å, Crystal structure of the human c5a in complex with MEDI7814 a neutralising antibody
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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