8Q6R: Complement FP

Structure of complement FP in complex with the TPP-3077 VHH. Determined by X-ray diffraction at 1.9 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Lama glama, Homo sapiens
Chains: 6
Atoms: 7,492
Mol. weight: 107.27 kDa
Ligands: NAG, MAN, GCH
Released: 28 Aug 2024

Explore 8Q6R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q6R contains 28 α-helices and 97 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.

Chains A and B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	10-12	3	2
β-strand	18-26	9	1
α-helix	28-30	3
β-strand	31-39	9	2
β-strand	46-52	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-99	9	2
α-helix	101-103	3
β-strand	107-109	3	2
β-strand	113-117	5	2

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	30-36	7	5
β-strand	43-51	9	5
α-helix	53-56	4
β-strand	63-65	3	5
β-strand	72-74	3	5
α-helix	77-78	2
β-strand	79-80	2	6
α-helix	81-89	9
β-strand	93	1	7
β-strand	96-103	8	8
β-strand	104-105	2	6
β-strand	111	1	9
β-strand	115	1	9
β-strand	120-127	8	8
β-strand	130	1	7

Chain D: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	260	1	10
β-strand	264-265	2	11
β-strand	275-281	7	11
β-strand	284	1	10
α-helix	288-289	2
α-helix	293-297	5
β-strand	301-307	7	11
α-helix	310-313	4
β-strand	314	1	12
β-strand	317-318	2	13
α-helix	323-327	5
β-strand	328	1	14
β-strand	342-347	6	14
β-strand	350-351	2	13
β-strand	354	1	12
α-helix	357-361	5
β-strand	362	1	2
β-strand	365-372	8	14
β-strand	377-379	3	15
β-strand	380-382	3	16
α-helix	383-388	6
β-strand	392	1	17
β-strand	400-406	7	17
β-strand	407-409	3	16
β-strand	417-418	2	18
β-strand	427-428	2	18
β-strand	429-432	4	14
β-strand	436-438	3	15
β-strand	442	1	19
β-strand	445	1	19
β-strand	448-454	7	17
α-helix	458-460	3

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	30-36	7	20
β-strand	43-51	9	20
α-helix	53-56	4
β-strand	63-65	3	20
β-strand	72-74	3	20
α-helix	77-78	2
β-strand	79-80	2	21
α-helix	81-89	9
β-strand	93	1	22
β-strand	95-103	9	23
β-strand	104-105	2	21
β-strand	111	1	24
β-strand	115	1	24
β-strand	120-128	9	23
β-strand	130	1	22

Chain F: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	260	1	25
β-strand	264-265	2	26
β-strand	275-281	7	26
β-strand	284	1	25
α-helix	288-289	2
α-helix	293-297	5
β-strand	301-307	7	26
α-helix	310-313	4
β-strand	314	1	27
β-strand	317-318	2	28
α-helix	323-326	4
β-strand	328	1	29
β-strand	342-347	6	29
β-strand	350-351	2	28
β-strand	354	1	27
α-helix	357-361	5
β-strand	362	1	4
β-strand	365-372	8	29
β-strand	377-379	3	30
β-strand	380-382	3	31
α-helix	383-388	6
β-strand	391	1	23
β-strand	392	1	32
β-strand	400-406	7	32
β-strand	407-409	3	31
β-strand	417-418	2	33
β-strand	427-428	2	33
β-strand	429-432	4	29
β-strand	436-438	3	30
β-strand	442	1	34
β-strand	445	1	34
β-strand	448-454	7	32
α-helix	458-460	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
The properdin specific VHH TPP-3077	A, B	protein	125	Lama glama
Properdin	C, E	protein	108	Homo sapiens	P27918 (AlphaFold model)
Properdin	D, F	protein	221	Homo sapiens	P27918 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8Q6R_1 The properdin specific VHH TPP-3077 (chains A, B)
EVQLLESGGGLVQPGGSLRLSCAASGRISSIIHMAWFRQAPGKERELVSEISRVGTTVYA
DSVKGRFTISRDNSKNTLYLQMNSLKPEDTAVYYCNALQYEKHGGADYWGQGTLVTVSSH
HHHHH

Sequence of entity 2 (C, E), FASTA

>8Q6R_2 Properdin (chains C, E)
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWA
PCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQACPE

Sequence of entity 3 (D, F), FASTA

>8Q6R_3 Properdin (chains D, F)
GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPV
DGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQ
HCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGR
PLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEELHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	20
GCH	Glycocholic acid	C26 H43 N O6	2

Primary citation

Characterization of the bispecific VHH antibody tarperprumig (ALXN1820) specific for properdin and designed for low-volume administration. Tamburini, P., Pedersen, D.V., Devore, D. et al. MAbs (2024) 16:2415060-2415060. DOI 10.1080/19420862.2024.2415060 · PubMed

Other PDB entries of the same protein (UniProt P27918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S08 2.03 Å, Crystal Structure of Properdin (TSR domains N1 & 456)
6S0B 2.31 Å, Crystal Structure of Properdin in complex with the CTC domain of C3/C3b
6S0A 2.52 Å, Crystal Structure of Properdin (TSR domains N12 & 456)
9U62 2.7 Å, AP pathways C3 convertase C3bBbP and C3 complex
6RUS 2.8 Å, Structure of a functional properdin monomer
7B26 3.4 Å, CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3
6SEJ 3.5 Å, Structure of a functional monomeric properdin lacking TSR3
6RV6 3.51 Å, Structure of properdin lacking TSR3 based on anomalous data
7NOZ 3.9 Å, Structure of the nanobody stablized properdin bound alternative pathway proconvertase…
6RUR 6.0 Å, Structure of the SCIN stabilized C3bBb convertase bound to properdin
6RUV 6.15 Å, Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the…
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and…

Browse structure collections

About this viewer

MolViewer shows 8Q6R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.