3L5N: Staphylococcal Complement Inhibitor

Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3b. Determined by X-ray diffraction at 7.54 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 7.54 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 3
Atoms: 12,785
Mol. weight: 186.37 kDa
Ligands: MAN, NAG
Released: 4 Aug 2010

Explore 3L5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L5N contains 30 α-helices and 139 β-strands across 2 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: 6 helices, 76 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-9	4	2
β-strand	12	1	3
β-strand	21	1	2
β-strand	25	1	1
β-strand	32-39	8	4
β-strand	51-53	3	4
β-strand	63	1	2
β-strand	83-90	8	4
β-strand	93-100	8	4
β-strand	101	1	3
β-strand	107	1	5
β-strand	110-112	3	6
β-strand	116-117	2	7
β-strand	119	1	8
β-strand	121	1	8
β-strand	122-123	2	9
β-strand	125-128	4	6
β-strand	130	1	5
β-strand	140	1	10
β-strand	141-143	3	11
β-strand	146	1	12
β-strand	152	1	12
β-strand	156	1	11
β-strand	159	1	10
β-strand	166-167	2	6
β-strand	171-172	2	9
α-helix	173-174	2
β-strand	180-181	2	7
β-strand	183	1	12
β-strand	184-188	5	11
β-strand	196-198	3	11
β-strand	201-202	2	7
β-strand	210-216	7	13
β-strand	230-237	8	13
β-strand	242	1	13
β-strand	245-247	3	14
β-strand	249-255	7	15
β-strand	258-267	10	15
β-strand	270-271	2	14
β-strand	272	1	16
β-strand	275	1	16
β-strand	276-279	4	13
α-helix	283-286	4
β-strand	298	1	17
β-strand	300	1	17
β-strand	301-303	3	15
β-strand	308-310	3	14
β-strand	316-317	2	14
β-strand	322-325	4	15
β-strand	332-334	3	18
β-strand	341	1	19
β-strand	348-350	3	20
β-strand	353-355	3	18
α-helix	360	1
β-strand	361	1	18
α-helix	362	1
β-strand	367-368	2	21
β-strand	387-389	3	20
β-strand	398-404	7	21
β-strand	416-421	6	21
β-strand	422	1	19
β-strand	425	1	22
β-strand	433-437	5	23
β-strand	448-449	2	24
β-strand	452-456	5	23
β-strand	467-474	8	25
β-strand	477-485	9	25
β-strand	494	1	23
β-strand	497-498	2	24
β-strand	506-508	3	26
β-strand	510-516	7	25
β-strand	522-527	6	25
β-strand	530-532	3	26
β-strand	541-543	3	27
β-strand	558-561	4	28
β-strand	563-565	3	27
β-strand	570-576	7	29
α-helix	591-600	10
β-strand	612	1	22
α-helix	615-618	4
β-strand	622-625	4	2

Chain B: 24 helices, 63 β-strands

Element	Residues	Length	Sheet
β-strand	741	1	30
β-strand	748-753	6	29
α-helix	759-760	2
β-strand	765-766	2	27
β-strand	769-772	4	28
β-strand	779-780	2	31
β-strand	781	1	29
β-strand	784-787	4	29
β-strand	793-795	3	29
β-strand	801-802	2	31
β-strand	810-812	3	32
β-strand	825	1	33
β-strand	826-828	3	32
β-strand	831	1	34
β-strand	838-839	2	35
β-strand	842-844	3	30
α-helix	845-846	2
β-strand	847	1	36
β-strand	850	1	36
β-strand	860-861	2	30
β-strand	865-866	2	35
β-strand	870	1	34
β-strand	876	1	33
β-strand	880	1	36
β-strand	884-885	2	37
β-strand	888-893	6	30
β-strand	900-905	6	30
β-strand	908-909	2	37
β-strand	915-916	2	38
β-strand	919-925	7	39
β-strand	937-940	4	40
α-helix	941-943	3
α-helix	948-949	2
β-strand	955-962	8	39
α-helix	991-994	4
α-helix	997-1007	11
α-helix	1012-1015	4
α-helix	1019-1022	4
α-helix	1030-1032	3
α-helix	1034-1036	3
α-helix	1051-1053	3
α-helix	1143-1156	14
α-helix	1157-1160	4
α-helix	1166-1174	9
α-helix	1183-1186	4
β-strand	1192-1193	2	41
β-strand	1197-1198	2	41
α-helix	1208-1220	13
α-helix	1227-1234	8
α-helix	1249-1263	15
β-strand	1272	1	42
β-strand	1275-1277	3	40
β-strand	1285-1286	2	40
β-strand	1289	1	42
β-strand	1300-1302	3	39
β-strand	1308-1311	4	40
β-strand	1318-1325	8	39
β-strand	1326-1327	2	38
β-strand	1339-1347	9	43
β-strand	1362-1370	9	43
β-strand	1376	1	44
β-strand	1379-1384	6	45
β-strand	1391	1	43
β-strand	1405-1406	2	45
α-helix	1409-1411	3
β-strand	1421-1423	3	45
β-strand	1425-1426	2	45
β-strand	1429	1	44
β-strand	1435-1436	2	43
β-strand	1439-1441	3	43
β-strand	1454-1459	6	45
β-strand	1467-1469	3	45
β-strand	1483-1485	3	46
β-strand	1488-1490	3	46
α-helix	1507-1513	7
β-strand	1519-1532	14	47
β-strand	1536-1548	13	47
β-strand	1559-1565	7	47
α-helix	1566-1568	3
β-strand	1579-1585	7	47
α-helix	1586-1588	3
β-strand	1592	1	48
β-strand	1595	1	48
β-strand	1598-1599	2	47
β-strand	1605-1609	5	47
α-helix	1621-1632	12
α-helix	1633-1637	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3	B	protein	915	Homo sapiens	P01024 (AlphaFold model)
Staphylococcal complement inhibitor	M	protein	88	Staphylococcus aureus	Q931M7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3L5N_1 Complement C3 (chains A)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 2 (B), FASTA

>3L5N_2 Complement C3 (chains B)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVA
QMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALEL
IKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLI
LEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGS
ITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLY
NVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD
HQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMY
HAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMM
TGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFN
VELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVT
LEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPI
KCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQD
LGAFTESMVVFGCPN

Sequence of entity 3 (M), FASTA

>3L5N_3 Staphylococcal complement inhibitor (chains M)
GSTSTSLPTSNEYQNEKLANELKSLLDELNVNELATGSLNTYYKRTIKISGQKAMYALKS
KDFKKMSEAKYQLQKIYNEIDEALKSKY

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b. Garcia, B.L., Ramyar, K.X., Tzekou, A. et al. J Mol Biol (2010) 402:17-29. DOI 10.1016/j.jmb.2010.07.029 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex

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