4D9Q: Factor D

Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D. Determined by X-ray diffraction at 2.28 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 2.28 Å
Organisms: Macaca mulatta, Homo sapiens
Chains: 6
Atoms: 10,620
Mol. weight: 143.37 kDa
Ligands: ZN
Released: 22 Feb 2012

Explore 4D9Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D9Q contains 59 α-helices and 127 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.

Chain A: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-61A	7
α-helix	63	1
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	104-108	5	3
β-strand	115	1	5
β-strand	120	1	5
α-helix	124	1
β-strand	124A	1	2
α-helix	125	1
α-helix	129A-131	3
β-strand	135-140	6	2
β-strand	154	1	4
β-strand	156-163	8	2
α-helix	165-169	5
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	208-213	6	2
α-helix	214-215	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-241	7

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	6
β-strand	20-21	2	7
α-helix	22-23	2
β-strand	30-35	6	8
β-strand	39-48	10	8
β-strand	51-54	4	8
α-helix	56-61A	7
α-helix	63	1
β-strand	64-68	5	8
β-strand	72	1	9
β-strand	81-90	10	8
β-strand	104-108	5	8
β-strand	115	1	10
β-strand	120	1	10
α-helix	124	1
β-strand	124A	1	7
α-helix	125	1
α-helix	129A-131	3
β-strand	135-140	6	7
β-strand	154	1	9
β-strand	156-163	8	7
α-helix	165-168	4
β-strand	180-183	4	7
β-strand	189	1	6
β-strand	198-201	4	7
β-strand	208-213	6	7
α-helix	214-215	2
α-helix	218-219	2
β-strand	226-230	5	7
α-helix	231-234	4
α-helix	235-242	8

Chains D and L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-65	4	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain E: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-51	6	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	110-111	2	17
β-strand	115-119	5	17
α-helix	123-124	2
β-strand	125	1	18
β-strand	128-132	5	19
β-strand	143-153	11	19
β-strand	154	1	18
β-strand	159-162	4	20
α-helix	163-165	3
β-strand	167	1	20
β-strand	171-173	3	19
α-helix	174-176	3
β-strand	177-178	2	19
β-strand	184-193	10	19
α-helix	196-199	4
β-strand	203-208	6	20
α-helix	209-211	3
β-strand	213-218	6	20

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
α-helix	7-9	3
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	46-51	6	22
β-strand	58-60	3	22
α-helix	62-64	3
β-strand	68-73	6	21
α-helix	74-76	3
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-98	7	22
β-strand	110-111	2	22
β-strand	115-119	5	22
α-helix	123-124	2
β-strand	125	1	23
β-strand	128-132	5	24
β-strand	139	1	24
β-strand	143-153	11	24
β-strand	154	1	23
β-strand	159-162	4	25
α-helix	163-165	3
β-strand	167	1	25
β-strand	172-173	2	24
α-helix	174-176	3
β-strand	177-178	2	24
β-strand	184-193	10	24
α-helix	196-199	4
β-strand	203-208	6	25
α-helix	209-211	3
β-strand	213-218	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Factor D	A, B	protein	228	Macaca mulatta	F6YBP7 (AlphaFold model)
Anti-Factor D, light chain	D, L	protein	213	Homo sapiens	Q8TCD0 (AlphaFold model)
Anti-Factor D, heavy chain	E, H	protein	217	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4D9Q_1 Factor D (chains A, B)
ILGGREAEAHARPYMASVQVNGEHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSL
SQPEPSKRLYDVLRAVPHPDSRPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVEPG
TLCDVAGWGIVSHAGRRPDRLQHVLLPVLDRATCNRRTHHDGAITQRMMCAESNRRDSCK
GDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA

Sequence of entity 2 (D, L), FASTA

>4D9Q_2 Anti-Factor D, light chain (chains D, L)
DIQVTQSPSSLSASVGDRVTITCITSTDIDDDMNWYQQKPGKVPKLLISGGNTLRPGVPS
RFSGSGSGTDFTLTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (E, H), FASTA

>4D9Q_3 Anti-Factor D, heavy chain (chains E, H)
EVQLVQSGPELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGETTY
ADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCEREGGVNNWGQGTLVTVSSASTKG
PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

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

Primary citation

Inhibiting alternative pathway complement activation by targeting the factor d exosite. Katschke, K.J., Wu, P., Ganesan, R. et al. J Biol Chem (2012) 287:12886-12892. DOI 10.1074/jbc.M112.345082 · PubMed

Browse structure collections

About this viewer

MolViewer shows 4D9Q 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.