6QSW: Complement factor B protease domain

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine. Determined by X-ray diffraction at 1.64 Å resolution. Released 27 Mar 2019.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,884
Mol. weight: 100.74 kDa
Ligands: JGT
Released: 27 Mar 2019

Explore 6QSW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QSW contains 40 α-helices and 45 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 AAA: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	1
β-strand	40-48	9	1
β-strand	51-54	4	1
α-helix	56-58	3
β-strand	64-68	5	1
α-helix	81-84	4
β-strand	85-90	6	1
α-helix	97C-97E	3
β-strand	104-108	5	1
α-helix	120-121	2
β-strand	122	1	2
β-strand	125A	1	3
α-helix	125B-125G	6
α-helix	125P-128	8
β-strand	133-142	10	2
β-strand	154-163	10	2
α-helix	165-170	6
α-helix	171-172B	4
α-helix	172L-174	3
β-strand	180-184	5	2
α-helix	192-194	3
α-helix	197	1
β-strand	198-203	6	2
β-strand	206-216	11	2
β-strand	225-230	6	2
α-helix	231-233	3
α-helix	235-241	7
β-strand	249	1	3

Chain BBB: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	4
β-strand	40-48	9	4
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	65-68	4	4
α-helix	81-84	4
β-strand	85-90	6	4
α-helix	97C-97E	3
β-strand	104-108	5	4
α-helix	120-121	2
β-strand	122	1	5
β-strand	125A	1	6
α-helix	125B-125G	6
α-helix	125P-128	8
β-strand	133-140	8	5
β-strand	156-163	8	5
α-helix	165-170	6
α-helix	171-172B	4
α-helix	172L-174	3
β-strand	180-184	5	5
α-helix	192-194	3
α-helix	197	1
β-strand	198-203	6	5
β-strand	206-216	11	5
β-strand	225-230	6	5
α-helix	231-233	3
α-helix	235-241	7
β-strand	249	1	6

Chain CCC: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	7
β-strand	40-48	9	7
β-strand	51-54	4	7
α-helix	56-58	3
β-strand	64-68	5	7
α-helix	81-84	4
β-strand	85-90	6	7
α-helix	97C-97E	3
β-strand	104-108	5	7
α-helix	120-121	2
β-strand	122	1	8
α-helix	123	1
β-strand	125A	1	9
α-helix	125B-125G	6
α-helix	125P-128	8
β-strand	133-142	10	8
β-strand	154-163	10	8
α-helix	165-170	6
α-helix	171-172B	4
α-helix	172L-174	3
β-strand	180-184	5	8
α-helix	192-194	3
α-helix	197	1
β-strand	198-203	6	8
β-strand	206-216	11	8
β-strand	225-230	6	8
α-helix	231-233	3
α-helix	235-241	7
β-strand	249	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement factor B	AAA, BBB, CCC	protein	291	Homo sapiens	P00751 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC), FASTA

>6QSW_1 Complement factor B (chains AAA, BBB, CCC)
SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDK
EHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIR
PICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKK
GSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQ
VGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL

Ligands and cofactors

ID	Name	Formula	Copies
JGT	~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine	C14 H14 Br N3	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Small-molecule factor B inhibitor for the treatment of complement-mediated diseases. Schubart, A., Anderson, K., Mainolfi, N. et al. Proc Natl Acad Sci U S A (2019) 116:7926-7931. DOI 10.1073/pnas.1820892116 · PubMed

Other PDB entries of the same protein (UniProt P00751 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RAV 1.7 Å, Complement factor B protease domain in complex with the reversible inhibitor…
6T8W 1.7 Å, Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidi…
6QSX 1.77 Å, Complement factor B protease domain in complex with the reversible inhibitor…
1Q0P 1.8 Å, A domain of Factor B
1RRK 2.0 Å, Crystal Structure Analysis of the Bb segment of Factor B
1DLE 2.1 Å, Factor B serine protease domain
3HRZ 2.2 Å, Cobra Venom Factor (CVF) in complex with human factor B
6T8V 2.29 Å, Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1…
1RTK 2.3 Å, Crystal Structure Analysis of the Bb segment of Factor B complexed with…
2OK5 2.3 Å, Human Complement factor B
1RS0 2.6 Å, Crystal Structure Analysis of the Bb segment of Factor B complexed with…
9U62 2.7 Å, AP pathways C3 convertase C3bBbP and C3 complex

Browse structure collections

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