8AYH: Complement C5

Structure of Complement C5 in Complex with small molecule inhibitor and CVF. Determined by electron microscopy at 3.35 Å resolution. Released 21 Dec 2022.

Method: Electron microscopy
Resolution: 3.35 Å
Organisms: Homo sapiens, Naja kaouthia
Chains: 3
Atoms: 19,109
Mol. weight: 371.45 kDa
Ligands: H1H, MG
Released: 21 Dec 2022

Explore 8AYH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AYH contains 62 α-helices and 206 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: 30 helices, 56 β-strands

Element	Residues	Length	Sheet
α-helix	682-688	7
α-helix	696-700	5
α-helix	722-736	15
α-helix	737-739	3
α-helix	744-753	10
α-helix	754-757	4
α-helix	759	1
α-helix	761-762	2
β-strand	764-765	2	7
α-helix	769-772	4
β-strand	776-781	6	18
β-strand	784-789	6	16
α-helix	790-791	2
β-strand	796-804	9	18
β-strand	809-811	3	18
α-helix	812-814	3
β-strand	815-818	4	18
β-strand	819	1	17
β-strand	823-827	5	19
β-strand	833-834	2	20
β-strand	838-839	2	21
β-strand	842-847	6	19
β-strand	853-855	3	22
β-strand	857-859	3	23
β-strand	886-888	3	22
α-helix	889	1
β-strand	892-897	6	19
β-strand	900	1	21
β-strand	906-907	2	20
β-strand	910-916	7	23
β-strand	919-925	7	23
β-strand	928-930	3	20
β-strand	935-944	10	24
β-strand	945	1	25
β-strand	954	1	25
β-strand	956-959	4	26
β-strand	967	1	27
α-helix	968	1
β-strand	974-980	7	24
α-helix	985-991	7
α-helix	1009-1012	4
α-helix	1016-1027	12
α-helix	1038-1054	17
β-strand	1060	1	28
β-strand	1066	1	28
β-strand	1067	1	29
β-strand	1074	1	29
α-helix	1076-1089	14
α-helix	1097-1110	14
β-strand	1112	1	30
β-strand	1118	1	30
β-strand	1131	1	31
α-helix	1133-1153	21
α-helix	1162-1177	16
α-helix	1185-1194	10
α-helix	1205-1214	10
β-strand	1217-1219	3	32
β-strand	1225-1227	3	32
α-helix	1245-1260	16
α-helix	1264-1277	14
α-helix	1288-1294	7
β-strand	1311	1	33
β-strand	1314-1316	3	26
β-strand	1325	1	26
β-strand	1328	1	33
α-helix	1335-1337	3
β-strand	1338-1340	3	24
β-strand	1346-1349	4	26
β-strand	1357-1366	10	24
β-strand	1367	1	27
β-strand	1375	1	34
β-strand	1377-1385	9	35
β-strand	1400-1408	9	35
α-helix	1409-1411	3
β-strand	1414	1	31
β-strand	1422-1427	6	34
α-helix	1428-1429	2
β-strand	1432-1434	3	36
α-helix	1436-1440	5
β-strand	1452-1456	5	34
β-strand	1459-1464	6	34
β-strand	1473-1478	6	35
β-strand	1479-1481	3	36
β-strand	1485-1486	2	21
β-strand	1491-1497	7	34
β-strand	1504-1509	6	34

Chain B: 19 helices, 89 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	37
β-strand	30	1	38
β-strand	32-33	2	39
β-strand	39-40	2	40
β-strand	42-46	5	37
β-strand	52-58	7	39
β-strand	69-75	7	39
β-strand	82-83	2	37
β-strand	86-87	2	40
β-strand	103-110	8	39
β-strand	113-121	9	39
α-helix	123-125	3
β-strand	128-130	3	41
β-strand	136-137	2	42
α-helix	142	1
β-strand	143	1	43
β-strand	147-149	3	41
β-strand	161-166	6	42
β-strand	172-178	7	42
β-strand	186	1	43
α-helix	187-189	3
α-helix	192-194	3
β-strand	195-203	9	42
β-strand	210-216	7	42
β-strand	224-230	7	44
β-strand	234-236	3	45
β-strand	243-251	9	44
β-strand	256	1	44
β-strand	259-268	10	45
β-strand	273-275	3	45
β-strand	283-285	3	45
β-strand	291-294	4	44
α-helix	296-300	5
α-helix	306-308	3
β-strand	313-322	10	45
β-strand	328-330	3	45
β-strand	336-339	4	45
β-strand	344-346	3	46
β-strand	360-367	8	46
β-strand	373	1	46
β-strand	380-381	2	47
β-strand	386-387	2	47
β-strand	395-400	6	46
β-strand	408-414	7	47
α-helix	422-424	3
β-strand	427-433	7	47
α-helix	434-435	2
β-strand	444-449	6	48
β-strand	454	1	49
β-strand	459-467	9	48
α-helix	473-475	3
β-strand	478-485	8	50
β-strand	488-496	9	50
β-strand	503-509	7	48
α-helix	512-514	3
β-strand	518-526	9	50
β-strand	530-534	5	50
β-strand	537-538	2	50
β-strand	540	1	49
β-strand	548-551	4	51
β-strand	556-557	2	52
β-strand	562-569	8	51
β-strand	574-576	3	53
β-strand	579-581	3	52
α-helix	582-585	4
α-helix	595-602	8
α-helix	617-622	6
β-strand	626	1	38
β-strand	629	1	37
α-helix	636-639	4
α-helix	746-747	2
β-strand	748	1	54
β-strand	754-755	2	52
β-strand	759-761	3	53
α-helix	765-766	2
β-strand	772	1	51
β-strand	775-779	5	51
β-strand	786-789	4	52
β-strand	792-795	4	53
β-strand	799-802	4	53
α-helix	803-805	3
β-strand	806-810	5	52
β-strand	814-817	4	55
β-strand	824-825	2	54
β-strand	830-838	9	55
β-strand	844-850	7	54
β-strand	856	1	56
β-strand	866-872	7	54
β-strand	876-884	9	55
β-strand	886	1	56
β-strand	890-900	11	54
β-strand	906-916	11	54
β-strand	1343-1350	8	57
β-strand	1363-1371	9	57
β-strand	1377-1385	9	58
β-strand	1390-1392	3	57
β-strand	1393	1	59
α-helix	1397-1400	4
β-strand	1406-1407	2	58
β-strand	1413-1414	2	59
β-strand	1417-1418	2	59
β-strand	1422-1430	9	58
β-strand	1438-1444	7	57
β-strand	1454-1459	6	58
β-strand	1468-1472	5	58
α-helix	1480-1482	3
β-strand	1483-1486	4	60
β-strand	1489-1492	4	60

Chain C: 13 helices, 61 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	50-57	8	3
β-strand	65-68	4	3
β-strand	71-73	3	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
α-helix	185-187	3
β-strand	188-189	2	6
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	9
β-strand	247-253	7	8
β-strand	259	1	8
β-strand	262-272	11	8
β-strand	280-282	3	8
β-strand	288-293	6	8
β-strand	296-300	5	8
α-helix	303-306	4
β-strand	321	1	9
β-strand	322-331	10	8
β-strand	337-342	6	8
β-strand	346-347	2	9
β-strand	352-356	5	10
β-strand	362-363	2	11
β-strand	369-377	9	10
β-strand	382	1	10
β-strand	387-391	5	12
β-strand	393-396	4	11
β-strand	401-403	3	11
α-helix	404-406	3
β-strand	407-410	4	12
β-strand	417-422	6	10
β-strand	428-431	4	11
β-strand	434-437	4	12
β-strand	449-451	3	12
β-strand	454-456	3	11
α-helix	457-458	2
β-strand	465-469	5	13
α-helix	475	1
β-strand	476	1	14
α-helix	477	1
β-strand	481-488	8	13
α-helix	493-495	3
β-strand	498-505	8	15
β-strand	508-516	9	15
α-helix	517-518	2
β-strand	524-529	6	13
β-strand	538-546	9	15
β-strand	553-561	9	15
β-strand	563	1	14
β-strand	572-576	5	16
β-strand	582	1	17
β-strand	587-593	7	16
β-strand	597-606	10	18
α-helix	607-609	3
α-helix	624-627	4
α-helix	628-630	3
α-helix	642-648	7
β-strand	651-654	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C5 beta chain	C	protein	657	Homo sapiens	P01031 (AlphaFold model)
Complement C5 alpha chain	A	protein	999	Homo sapiens	P01031 (AlphaFold model)
Cobra venom factor	B	protein	1642	Naja kaouthia	Q91132 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>8AYH_1 Complement C5 beta chain (chains C)
QEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENK
FQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPD
QSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGM
WTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNK
VVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDL
NNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS
LDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTD
APDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDKITH
YNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDS
VWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGVQRGAKK
PLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANADDSQENDEPCKEILRP

Sequence of entity 2 (A), FASTA

>8AYH_2 Complement C5 alpha chain (chains A)
TLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQ
LRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTW
EIQGVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQFCV
KMSAVEGICTSESPVIDHQGTKSSKCVRQKVEGSSSHLVTFTVLPLEIGLHNINFSLETW
FGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFPYRIPLDLVPKTEIKRIL
SVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSD
PLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQ
NSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFD
ICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREAL
VKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEE
QRYGGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHKGALHNYKMTDKNFLGRP
VEVLLNDDLIVSTGFGSGLATVHVTTVVHKTSTSEEVCSFYLKIDTQDIEASHYRGYGNS
DYKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLKALVEGVDQLFTDYQIKD
GHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHRPDKQCTMFYSTSNIKIQ
KVCEGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYAYKVSITSITVENVFVKY
KATLLDIYKTGEAVAEKDSEITFIKKVTCTNAELVKGRQYLIMGKEALQIKYNFSFRYIY
PLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGC

Sequence of entity 3 (B), FASTA

>8AYH_3 Cobra venom factor (chains B)
MERMALYLVAALLIGFPGSSHGALYTLITPAVLRTDTEEQILVEAHGDSTPKQLDIFVHD
FPRKQKTLFQTRVDMNPAGGMLVTPTIEIPAKEVSTDSRQNQYVVVQVTGPQVRLEKVVL
LSYQSSFLFIQTDKGIYTPGSPVLYRVFSMDHNTSKMNKTVIVEFQTPEGILVSSNSVDL
NFFWPYNLPDLVSLGTWRIVAKYEHSPENYTAYFDVRKYVLPSFEVRLQPSEKFFYIDGN
ENFHVSITARYLYGEEVEGVAFVLFGVKIDDAKKSIPDSLTRIPIIDGDGKATLKRDTFR
SRFPNLNELVGHTLYASVTVMTESGSDMVVTEQSGIHIVASPYQIHFTKTPKYFKPGMPY
ELTVYVTNPDGSPAAHVPVVSEAFHSMGTTLSDGTAKLILNIPLNAQSLPITVRTNHGDL
PRERQATKSMTAIAYQTQGGSGNYLHVAITSTEIKPGDNLPVNFNVKGNANSLKQIKYFT
YLILNKGKIFKVGRQPRRDGQNLVTMNLHITPDLIPSFRFVAYYQVGNNEIVADSVWVDV
KDTCMGTLVVKGDNLIQMPGAAMKIKLEGDPGARVGLVAVDKAVYVLNDKYKISQAKIWD
TIEKSDFGCTAGSGQNNLGVFEDAGLALTTSTNLNTKQRSAAKCPQPANRRRRSSVLLLD
SNASKAAEFQDQDLRKCCEDVMHENPMGYTCEKRAKYIQEGDACKAAFLECCRYIKGVRD
ENQRESELFLARDDNEDGFIADSDIISRSDFPKSWLWLTKDLTEEPNSQGISSKTMSFYL
RDSITTWVVLAVSFTPTKGICVAEPYEIRVMKVFFIDLQMPYSVVKNEQVEIRAILHNYV
NEDIYVRVELLYNPAFCSASTKGQRYRQQFPIKALSSRAVPFVIVPLEQGLHDVEIKASV
QEALWSDGVRKKLKVVPEGVQKSIVTIVKLDPRAKGVGGTQLEVIKARKLDDRVPDTEIE
TKIIIQGDPVAQIIENSIDGSKLNHLIITPSGCGEQNMIRMAAPVIATYYLDTTEQWETL
GINRRTEAVNQIVTGYAQQMVYKKADHSYAAFTNRASSSWLTAYVVKVFAMAAKMVAGIS
HEIICGGVRWLILNRQQPDGAFKENAPVLSGTMQGGIQGAEEEVYLTAFILVALLESKTI
CNDYVNSLDSSIKKATNYLLKKYEKLQRPYTTALTAYALAAADQLNDDRVLMAASTGRDH
WEEYNAHTHNIEGTSYALLALLKMKKFDQTGPIVRWLTDQNFYGETYGQTQATVMAFQAL
AEYEIQMPTHKDLNLDITIELPDREVPIRYRINYENALLARTVETKLNQDITVTASGDGK
ATMTILTFYNAQLQEKANVCNKFHLNVSVENIHLNAMGAKGALMLKICTRYLGEVDSTMT
IIDISMLTGFLPDAEDLTRLSKGVDRYISRYEVDNNMAQKVAVIIYLNKVSHSEDECLHF
KILKHFEVGFIQPGSVKVYSYYNLDEKCTKFYHPDKGTGLLNKICIGNVCRCAGETCSSL
NHQERIDVPLQIEKACETNVDYVYKTKLLRIEEQDGNDIYVMDVLEVIKQGTDENPRAKT
HQYISQRKCQEALNLKVNDDYLIWGSRSDLLPTKDKISYIITKNTWIERWPHEDECQEEE
FQKLCDDFAQFSYTLTEFGCPT

Ligands and cofactors

ID	Name	Formula	Copies
H1H	5-methoxy-2-[[(1~{S})-1-(2-methoxyphenyl)ethyl]carbamoylamino]-4-(4-methylpento…	C24 H32 N2 O6	1
MG	Magnesium ion	Mg	1

Primary citation

A small-molecule inhibitor of C5 complement protein. Jendza, K., Kato, M., Salcius, M. et al. Nat Chem Biol (2019) 15:666-668. DOI 10.1038/s41589-019-0303-9 · 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
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…

Browse structure collections

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