6WRV: Computationally designed protein 3DS18

Crystal structure of computationally designed protein 3DS18 in complex with the human Transferrin receptor ectodomain. Determined by X-ray diffraction at 2.47 Å resolution. Released 28 Apr 2021.

Method: X-ray diffraction
Resolution: 2.47 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 17,774
Mol. weight: 253.31 kDa
Ligands: CA
Released: 28 Apr 2021

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

Secondary structure: helices and β-sheets

6WRV contains 107 α-helices and 87 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: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	124-136	13
α-helix	140-147	8
α-helix	160-175	16
β-strand	180-192	13	1
α-helix	197-198	2
β-strand	199-204	6	2
β-strand	209-214	6	2
β-strand	220-221	2	3
β-strand	226-230	5	2
β-strand	232-234	3	4
α-helix	240-244	5
β-strand	254-258	5	4
α-helix	264-273	10
β-strand	278-282	5	4
β-strand	297	1	5
β-strand	299-300	2	3
α-helix	317-319	3
β-strand	334-336	3	4
α-helix	339-346	8
β-strand	349-352	4	4
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-367	4	4
β-strand	371-377	7	2
β-strand	380-393	14	1
β-strand	398-408	11	1
α-helix	416-420	5
α-helix	421-439	19
β-strand	446-453	8	1
α-helix	456-458	3
α-helix	461-469	9
α-helix	471-474	4
β-strand	478-483	6	1
β-strand	488	1	1
β-strand	493-498	6	1
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	6
α-helix	515	1
β-strand	521	1	6
α-helix	528-531	4
α-helix	532-535	4
α-helix	541-546	6
β-strand	552-558	7	1
α-helix	562-563	2
β-strand	568	1	5
α-helix	573-579	7
α-helix	583-602	20
α-helix	613-626	14
α-helix	629-634	6
α-helix	640-662	23
α-helix	668-679	12
α-helix	683-685	3
β-strand	686	1	7
β-strand	699	1	7
α-helix	709-717	9
α-helix	728-750	23
α-helix	753-755	3

Chain B: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	124-136	13
α-helix	140-147	8
α-helix	160-175	16
β-strand	180-192	13	8
α-helix	197-198	2
β-strand	199-204	6	9
β-strand	209-214	6	9
β-strand	220-221	2	10
β-strand	226-230	5	9
β-strand	232-234	3	11
α-helix	240-244	5
β-strand	254-258	5	11
α-helix	264-273	10
β-strand	278-282	5	11
β-strand	297	1	12
β-strand	299-300	2	10
α-helix	317-319	3
β-strand	334-336	3	11
α-helix	339-346	8
β-strand	349-352	4	11
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-367	4	11
β-strand	371-377	7	9
β-strand	380-393	14	8
β-strand	398-408	11	8
α-helix	416-420	5
α-helix	421-438	18
β-strand	446-453	8	8
α-helix	456-458	3
α-helix	461-469	9
α-helix	471-474	4
β-strand	478-483	6	8
β-strand	488	1	8
β-strand	493-498	6	8
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	13
α-helix	515	1
β-strand	521	1	13
α-helix	528-531	4
α-helix	532-535	4
α-helix	541-546	6
β-strand	552-558	7	8
α-helix	562-563	2
β-strand	568	1	12
α-helix	573-579	7
α-helix	583-602	20
α-helix	613-626	14
α-helix	629-634	6
α-helix	640-662	23
α-helix	668-679	12
α-helix	683-685	3
β-strand	686	1	14
β-strand	699	1	14
α-helix	709-720	12
α-helix	728-750	23
α-helix	753-755	3

Chains C, D and F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-20	19
α-helix	25-35	11
β-strand	40-43	4	9
α-helix	47-60	14
β-strand	65-69	5	9
β-strand	72-76	5	9
α-helix	80-92	13

Chain E: 31 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	124-136	13
α-helix	140-147	8
α-helix	160-175	16
β-strand	180-192	13	15
α-helix	197-198	2
β-strand	199-204	6	16
β-strand	209-214	6	16
β-strand	220-221	2	17
β-strand	226-230	5	16
β-strand	232-234	3	18
α-helix	240-244	5
β-strand	254-258	5	18
α-helix	264-273	10
β-strand	278-282	5	18
β-strand	297	1	19
β-strand	299-300	2	17
α-helix	317-319	3
β-strand	334-336	3	18
α-helix	339-346	8
β-strand	349-352	4	18
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-367	4	18
β-strand	371-377	7	16
β-strand	380-393	14	15
β-strand	402-408	7	15
α-helix	416-420	5
α-helix	421-438	18
β-strand	447-453	7	15
α-helix	456-458	3
α-helix	461-474	14
β-strand	478-483	6	15
β-strand	488	1	15
β-strand	493-498	6	15
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	20
α-helix	515	1
β-strand	521	1	20
α-helix	528-531	4
α-helix	532-535	4
α-helix	541-546	6
β-strand	552-558	7	15
α-helix	562-563	2
β-strand	568	1	19
α-helix	573-579	7
α-helix	583-602	20
α-helix	613-626	14
α-helix	629-634	6
α-helix	640-662	23
α-helix	668-679	12
α-helix	683-685	3
β-strand	686	1	21
β-strand	699	1	21
α-helix	709-717	9
α-helix	728-750	23
α-helix	753-755	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transferrin receptor protein 1	A, B, E	protein	639	Homo sapiens	P02786 (AlphaFold model)
Computationally designed protein 3DS18	C, D, F	protein	94	synthetic construct

Sequence of entity 1 (A, B, E), FASTA

>6WRV_1 Transferrin receptor protein 1 (chains A, B, E)
RLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSK
VWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTK
KDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGH
AHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTD
STCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSG
VGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFT
YINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNA
AFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIK
LTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDF
GNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRK
QNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNE

Sequence of entity 2 (C, D, F), FASTA

>6WRV_2 Computationally designed protein 3DS18 (chains C, D, F)
DEREEEQRRRLEEVKEEAKRRERSEQDLAVLYLEAVNAAVVFVADSEEEAKRVADIVKKL
VPEVIIFVHDNFVVFVVDSDEAARRVYEIVERAQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

Transferrin receptor targeting by de novo sheet extension. Sahtoe, D.D., Coscia, A., Mustafaoglu, N. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2021569118 · PubMed

Other PDB entries of the same protein (UniProt P02786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OKD 1.85 Å, Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide
8P0Z 1.88 Å, AP01-S2.3 - a variant of a redesigned transferrin receptor apical domain
6Y76 1.98 Å, AP01 - a redesigned transferrin receptor apical domain
9GH7 2.08 Å, Complex of human TfR1 with a potent bicyclic peptide
11QC 2.4 Å, Human transferrin receptor ectodomain
11RN 2.4 Å, Complex of B19V VP1u RBD and human transferrin receptor ectodomain
3KAS 2.4 Å, Machupo virus GP1 bound to human transferrin receptor 1
7ZQS 2.54 Å, Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer
1DE4 2.8 Å, Hemochromatosis protein hfe complexed with transferrin receptor
6WRW 2.84 Å, Crystal structure of computationally designed protein 2DS25.5 in complex with the human…
6WRX 3.07 Å, Crystal structure of computationally designed protein 2DS25.1 in complex with the human…
1CX8 3.2 Å, Crystal structure of the ectodomain of human transferrin receptor

Browse structure collections

About this viewer

MolViewer shows 6WRV 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.