1OK9: Complement decay-accelerating factor

Decay accelerating factor (CD55): The structure of an intact human complement regulator. Determined by X-ray diffraction at 3.0 Å resolution. Released 7 Jan 2004.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,991
Mol. weight: 57.49 kDa
Ligands: PT
Released: 7 Jan 2004

Explore 1OK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1OK9 contains 18 α-helices and 77 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: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	7-8	2
β-strand	13-15	3	2
β-strand	23-24	2	1
β-strand	28-30	3	3
β-strand	31-33	3	2
β-strand	37-39	3	4
α-helix	40	1
β-strand	46-48	3	3
β-strand	49-50	2	5
β-strand	54-55	2	5
α-helix	56-57	2
β-strand	62-64	3	4
β-strand	65	1	6
β-strand	75-77	3	7
α-helix	81-83	3
β-strand	88	1	6
β-strand	92-94	3	8
β-strand	95-97	3	7
β-strand	101-103	3	9
β-strand	110-112	3	8
β-strand	113	1	10
β-strand	119	1	10
α-helix	120-122	3
β-strand	126-128	3	9
α-helix	129	1
β-strand	130	1	11
α-helix	131-133	3
β-strand	140-143	4	12
β-strand	149	1	11
β-strand	153-158	6	12
β-strand	162-165	4	13
β-strand	169-171	3	12
β-strand	172-175	4	14
β-strand	178-181	4	14
β-strand	187-190	4	13
α-helix	191	1
β-strand	193	1	15
β-strand	202-204	3	16
β-strand	211	1	15
β-strand	216-218	3	17
β-strand	219-221	3	16
β-strand	226-228	3	18
β-strand	229-230	2	19
β-strand	232-234	3	17
β-strand	235-238	4	20
β-strand	241-244	4	20
α-helix	247-249	3
β-strand	250-252	3	18

Chain B: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	21
α-helix	7-8	2
β-strand	13-15	3	22
β-strand	23	1	21
β-strand	28-30	3	23
β-strand	31-33	3	22
β-strand	37-39	3	24
α-helix	40	1
β-strand	46-48	3	23
β-strand	49-50	2	25
β-strand	54-55	2	25
α-helix	56-57	2
β-strand	62-64	3	24
β-strand	65	1	26
α-helix	66-71	6
β-strand	75-77	3	27
α-helix	81-83	3
β-strand	88	1	26
β-strand	92-94	3	28
β-strand	95-97	3	27
β-strand	101-103	3	29
β-strand	110-112	3	28
β-strand	113	1	30
β-strand	119	1	30
α-helix	120-122	3
β-strand	126-128	3	29
α-helix	129	1
β-strand	130	1	31
α-helix	131-133	3
β-strand	140-144	5	19
β-strand	149	1	31
β-strand	153-158	6	19
β-strand	162-165	4	32
β-strand	169-171	3	19
β-strand	172-175	4	33
β-strand	178-181	4	33
β-strand	187-190	4	32
α-helix	191	1
β-strand	193	1	34
β-strand	202-204	3	35
β-strand	211	1	34
β-strand	216-218	3	36
β-strand	219-221	3	35
β-strand	232-234	3	36
β-strand	235-236	2	37
β-strand	243-244	2	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement decay-accelerating factor	A, B	protein	254	HOMO SAPIENS	P08174 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1OK9_1 COMPLEMENT DECAY-ACCELERATING FACTOR (chains A, B)
MQDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEE
FCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWS
TAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQ
WSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNND
EGEWSGPPPECRGC

Ligands and cofactors

ID	Name	Formula	Copies
PT	Platinum (II) ion	Pt	2

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

Primary citation

Complement Regulation at the Molecular Level: The Structure of Decay-Accelerating Factor. Lukacik, P., Roversi, P., White, J. et al. Proc Natl Acad Sci U S A (2004) 101:1279. DOI 10.1073/PNAS.0307200101 · PubMed

Other PDB entries of the same protein (UniProt P08174 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1H03 1.7 Å, Human CD55 domains 3 & 4
1H04 2.0 Å, Human CD55 domains 3 & 4
1OK3 2.2 Å, Decay accelerating factor (cd55): the structure of an intact human complement regulator.
1OJV 2.3 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OJW 2.3 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OK2 2.5 Å, Decay accelerating factor (CD55): the structure of an intact human complement regulator.
1OJY 2.6 Å, Decay accelerating factor (cd55): the structure of an intact human complement regulator.
1OK1 2.6 Å, Decay accelerating factor (cd55) : the structure of an intact human complement regulator.
8K9T 2.66 Å, Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
8K9R 2.68 Å, Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
1H2P 2.8 Å, Human CD55 domains 3 & 4
6LA5 2.86 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4

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