7OP0: Complement C5

Crystal structure of complement C5 in complex with chemically synthesized K92 knob domain. Determined by X-ray diffraction at 2.57 Å resolution. Released 6 Apr 2022.

Method: X-ray diffraction
Resolution: 2.57 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 13,067
Mol. weight: 190.49 kDa
Released: 6 Apr 2022

Explore 7OP0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OP0 contains 53 α-helices and 121 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: 38 helices, 61 β-strands

Element	Residues	Length	Sheet
α-helix	684-688	5
α-helix	696-703	8
α-helix	711-714	4
α-helix	722-738	17
α-helix	744-753	10
α-helix	760-761	2
β-strand	764-765	2	1
α-helix	770-772	3
β-strand	773	1	2
β-strand	777-780	4	2
β-strand	783-789	7	3
β-strand	796-805	10	2
β-strand	808-811	4	2
α-helix	812-814	3
β-strand	815-818	4	2
β-strand	819	1	4
β-strand	823-828	6	5
β-strand	833-834	2	6
β-strand	838-847	10	5
β-strand	853-861	9	6
β-strand	865-866	2	7
β-strand	886-888	3	6
β-strand	892-900	9	5
β-strand	901-902	2	7
β-strand	906-916	11	6
β-strand	920-930	11	6
β-strand	934-944	11	8
β-strand	945	1	9
β-strand	954	1	9
β-strand	956-959	4	10
β-strand	967	1	8
α-helix	968	1
β-strand	974-980	7	8
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	11
β-strand	1066	1	11
β-strand	1067	1	12
β-strand	1074	1	12
α-helix	1076-1089	14
α-helix	1097-1110	14
β-strand	1112	1	13
β-strand	1118	1	13
β-strand	1130	1	14
α-helix	1133-1154	22
α-helix	1156-1158	3
α-helix	1162-1178	17
α-helix	1180	1
α-helix	1182	1
α-helix	1185-1196	12
α-helix	1203-1213	11
β-strand	1217-1219	3	15
β-strand	1225-1227	3	15
α-helix	1245-1260	16
α-helix	1264-1276	13
α-helix	1278-1279	2
α-helix	1288-1303	16
α-helix	1307-1309	3
β-strand	1310	1	16
β-strand	1311-1317	7	10
β-strand	1322-1328	7	10
β-strand	1334	1	8
α-helix	1335-1337	3
β-strand	1338-1340	3	8
β-strand	1346-1349	4	10
β-strand	1354	1	16
β-strand	1357-1367	11	8
β-strand	1375	1	17
β-strand	1377-1386	10	18
β-strand	1399-1408	10	18
β-strand	1414	1	14
β-strand	1422-1427	6	17
α-helix	1428-1429	2
β-strand	1432-1434	3	18
α-helix	1436-1444	9
β-strand	1452-1456	5	17
β-strand	1459-1464	6	17
β-strand	1473-1481	9	18
β-strand	1485-1486	2	5
β-strand	1491-1497	7	17
β-strand	1504-1509	6	17
α-helix	1533-1534	2
β-strand	1535	1	19
α-helix	1536-1537	2
α-helix	1547-1552	6
β-strand	1560-1571	12	19
β-strand	1574-1586	13	19
α-helix	1592-1593	2
β-strand	1597-1603	7	19
α-helix	1611-1612	2
β-strand	1616-1620	5	19
β-strand	1625-1626	2	19
β-strand	1635-1638	4	19
β-strand	1644-1648	5	19
α-helix	1657-1673	17

Chain B: 15 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	20
β-strand	31-32	2	21
β-strand	36-44	9	20
β-strand	50-58	9	22
β-strand	65-73	9	22
α-helix	75-77	3
β-strand	80-86	7	20
α-helix	89-91	3
β-strand	101-108	8	22
β-strand	112-118	7	22
β-strand	119-120	2	21
β-strand	125-130	6	23
β-strand	134-135	2	24
β-strand	140-141	2	25
β-strand	143-148	6	23
β-strand	154	1	23
β-strand	159-164	6	24
β-strand	170-176	7	24
β-strand	182-184	3	23
α-helix	185-187	3
β-strand	188-189	2	25
α-helix	190-191	2
β-strand	197-205	9	24
β-strand	212-219	8	24
β-strand	221-222	2	1
β-strand	227-233	7	26
β-strand	238	1	27
α-helix	241-243	3
β-strand	246-254	9	26
β-strand	259	1	26
β-strand	262-272	11	28
β-strand	282	1	28
β-strand	288-293	6	28
β-strand	296	1	28
β-strand	298-301	4	26
α-helix	303-306	4
β-strand	322-331	10	28
β-strand	337-346	10	28
β-strand	347	1	27
β-strand	353-356	4	29
β-strand	362-363	2	30
β-strand	369-370	2	31
β-strand	373-376	4	29
β-strand	382	1	29
β-strand	388-396	9	30
β-strand	402	1	30
α-helix	403-405	3
β-strand	407-409	3	30
α-helix	410-412	3
β-strand	418	1	29
β-strand	421-422	2	31
β-strand	428-437	10	30
α-helix	444-446	3
β-strand	449-456	8	30
α-helix	457-458	2
β-strand	464-468	5	32
β-strand	481-489	9	32
β-strand	498-505	8	33
β-strand	508-516	9	33
α-helix	517-518	2
β-strand	524-529	6	32
α-helix	532-534	3
β-strand	537-546	10	33
β-strand	553-562	10	33
β-strand	571-576	6	3
β-strand	582	1	4
β-strand	587-594	8	3
β-strand	598-606	9	2
α-helix	607-609	3
α-helix	626-630	5
α-helix	642-648	7
β-strand	651-655	5	20

Chain C: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	34
β-strand	6	1	34
β-strand	25	1	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C5 alpha chain	A	protein	999	Homo sapiens	P01031 (AlphaFold model)
Complement C5 beta chain	B	protein	657	Homo sapiens	P01031 (AlphaFold model)
K92chemFE	C	protein	35	Bos taurus

Sequence of entity 1 (A), FASTA

>7OP0_1 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 2 (B), FASTA

>7OP0_2 Complement C5 beta chain (chains B)
QEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENK
FQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPD
QSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGM
WTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNK
VVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDL
NNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS
LDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTD
APDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDKITH
YNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDS
VWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGVQRGAKK
PLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANADDSQENDEPCKEILRP

Sequence of entity 3 (C), FASTA

>7OP0_3 K92chemFE (chains C)
TCPEGWSECGVAIYGYACGRWGCGHFLNSGPNISP

Primary citation

The Chemical Synthesis of Knob Domain Antibody Fragments. Macpherson, A., Birtley, J.R., Broadbridge, R.J. et al. ACS Chem Biol (2021) 16:1757-1769. DOI 10.1021/acschembio.1c00472 · 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
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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