5B4P: Repebody

Complex structure of human C5a and its binding repebody. Determined by X-ray diffraction at 2.4 Å resolution. Released 12 Apr 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: synthetic construct, Homo sapiens
Chains: 4
Atoms: 5,157
Mol. weight: 76.08 kDa
Released: 12 Apr 2017

Explore 5B4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B4P contains 23 α-helices and 30 β-strands across 4 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
α-helix	9-12	4
α-helix	16-25	10
β-strand	34	1	1
α-helix	37-42	6
β-strand	45-49	5	2
β-strand	67-75	9	2
α-helix	78-81	4
β-strand	89-97	9	2
α-helix	103-106	4
β-strand	112-114	3	2
β-strand	118	1	2
α-helix	123-124	2
β-strand	136-138	3	2
β-strand	160-162	3	2
β-strand	184-186	3	2
β-strand	209-210	2	2
β-strand	216	1	3
α-helix	224-231	8
β-strand	236	1	2
β-strand	245	1	3

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-10	9
α-helix	16-26	11
α-helix	34-39	6
α-helix	45-63	19

Chain C: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	4
α-helix	9-12	4
α-helix	16-26	11
β-strand	34-35	2	4
α-helix	37-42	6
β-strand	45-49	5	5
β-strand	55	1	6
α-helix	59-61	3
β-strand	67-75	9	5
β-strand	76	1	6
α-helix	78-81	4
β-strand	89-97	9	5
β-strand	112-114	3	5
β-strand	118	1	5
β-strand	136-138	3	5
β-strand	160-162	3	5
β-strand	184-186	3	5
β-strand	208-210	3	5
β-strand	216	1	7
α-helix	225-232	8
β-strand	236	1	5
α-helix	240-242	3
β-strand	245	1	7

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-12	11
α-helix	16-26	11
α-helix	34-40	7
α-helix	45-62	18
α-helix	67-70	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
repebody	A, C	protein	261	synthetic construct
C5a anaphylatoxin	B, D	protein	75	Homo sapiens	P01031 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5B4P_1 repebody (chains A, C)
ALETITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQG
IQYLPNVRYLALGGNKLHDISALKELTNLTYLFLDFNQLQLPNGVFDKLTNLKELYLSPN
QLQSLPDGVFDKLTNLTILGLDMNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPKGVFDK
LTQLKDLSLSYNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVG
GPDSAKCSGSGKPVRSIICPT

Sequence of entity 2 (B, D), FASTA

>5B4P_2 C5a anaphylatoxin (chains B, D)
STLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVAS
QLRANISHKDMQLGR

Primary citation

Complex structure of human C5a and its binding repebody. Kim, H.-S., Choi, J.M., Hwang, D.E. To be published.

Other PDB entries of the same protein (UniProt P01031 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Y6C 2.0 Å, X-ray structure analysis of human Complement Component 5 TE domain in complex with the…
5B71 2.11 Å, Crystal structure of complement C5 in complex with SKY59
4UU9 2.12 Å, Crystal structure of the human c5a in complex with MEDI7814 a neutralising antibody
7AD7 2.3 Å, Crystal structure of human complement C5 in complex with the K8 bovine knob domain…
4P39 2.4 Å, Crystal structure of the human C5aR antagonist C5a-A8
7OP0 2.57 Å, Crystal structure of complement C5 in complex with chemically synthesized K92 knob domain.
3HQA 2.59 Å, Crystal structure of human desarg-C5A
5HCC 2.59 Å, Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Dermacentor…
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
6RPT 2.7 Å, Structure of tick complement inhibitor CirpT1 complexed with macroglobubulin domain 4 of…
7AD6 2.75 Å, Crystal structure of human complement C5 in complex with the K92 bovine knob domain…
22GK 2.84 Å, C5a bound C5aR2 in complex with beta-arrestin1

Browse structure collections

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