5F3J: DBP

Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10. Determined by X-ray diffraction at 4.0 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 4.0 Å
Organisms: Plasmodium vivax (strain Salvador I), Mus musculus
Chains: 4
Atoms: 7,719
Mol. weight: 139.68 kDa
Released: 18 May 2016

Explore 5F3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F3J contains 35 α-helices and 58 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: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	220-222	3
β-strand	229	1	1
β-strand	238	1	1
α-helix	240-243	4
α-helix	268-290	23
α-helix	297-315	19
α-helix	325-336	12
α-helix	342-359	18
α-helix	388-414	27
α-helix	430-461	32
α-helix	474-481	8
α-helix	487-494	8

Chain B: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	220-222	3
β-strand	229	1	2
β-strand	238	1	2
α-helix	240-243	4
α-helix	268-290	23
α-helix	297-314	18
α-helix	325-336	12
α-helix	342-362	21
α-helix	388-414	27
β-strand	418	1	3
β-strand	424	1	3
α-helix	430-461	32
α-helix	475-481	7
α-helix	487-494	8
α-helix	501-505	5

Chain C: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	4
α-helix	51-52	2
β-strand	53	1	5
β-strand	58	1	6
β-strand	61-64	4	4
β-strand	77-82	6	7
β-strand	88-93	6	7
α-helix	97	1
β-strand	98	1	7
α-helix	99	1
β-strand	106-107	2	6
β-strand	110	1	4
β-strand	114-116	3	4
β-strand	118-119	2	6
β-strand	129-134	6	7
α-helix	140	1
β-strand	141	1	8
β-strand	146	1	7
β-strand	151	1	5
β-strand	173-175	3	9
β-strand	179-180	2	10
β-strand	188-193	6	9
α-helix	196-198	3
β-strand	201-208	8	8
β-strand	214-221	8	8
β-strand	226-229	4	8
β-strand	237-242	6	9
β-strand	247-252	6	9
α-helix	257-259	3
β-strand	262-269	8	8
β-strand	276-279	4	8
β-strand	283-284	2	8
β-strand	285-286	2	10

Chain D: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	11
α-helix	51-53	3
β-strand	58	1	12
β-strand	61-64	4	11
β-strand	77-82	6	13
β-strand	88-92	5	13
α-helix	97	1
β-strand	98	1	13
α-helix	99	1
β-strand	106-107	2	12
β-strand	110	1	11
β-strand	114-116	3	11
β-strand	118-119	2	12
β-strand	129-134	6	13
α-helix	140	1
β-strand	141-142	2	13
β-strand	146	1	13
β-strand	173-175	3	14
β-strand	179	1	15
β-strand	187-193	7	14
α-helix	196-198	3
β-strand	201-208	8	13
β-strand	214-221	8	13
β-strand	226-229	4	13
α-helix	231-233	3
β-strand	237-242	6	14
β-strand	247-252	6	14
α-helix	253-254	2
α-helix	257-259	3
β-strand	262-269	8	13
β-strand	276-279	4	13
β-strand	283-284	2	13
β-strand	285	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Duffy receptor	A, B	protein	317	Plasmodium vivax (strain Salvador I)	P22290 (AlphaFold model)
Antibody 2D10 single chain variable fragment	C, D	protein	305	Mus musculus

Sequence of entity 1 (A, B), FASTA

>5F3J_1 Duffy receptor (chains A, B)
ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFR
KLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVV
ENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQ
IYRWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKN
QWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS
VEEAKKNTQEVVTNVDN

Sequence of entity 2 (C, D), FASTA

>5F3J_2 Antibody 2D10 single chain variable fragment (chains C, D)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGLAAQPAMADIVITQDELSNPVTSGESVSI
SCRSSKSLLYQDGKTYLNWFLQRPGQSPQLLIYLMSTRASGVSDRFSGSGSGTDFTLEIS
RVEAEDVGVYYCQQLVEYPLTFGAGTKLELKRADGGGGSGGGGSGGGGSQVQLQQSGPEL
VKPGASVKISCKASGYAFISSWMNWVKQRPGKGLEWIGRIYPGDGDTHYNGKFKGKATLT
ADKSSSTAYMQLSSLTSEDSAVYFCAREETAQTGGFDYWGQGTTLTVSSEASGADHGTKH
HHHHH

Primary citation

Broadly neutralizing epitopes in the Plasmodium vivax vaccine candidate Duffy Binding Protein. Chen, E., Salinas, N.D., Huang, Y. et al. Proc Natl Acad Sci U S A (2016) 113:6277-6282. DOI 10.1073/pnas.1600488113 · PubMed

Other PDB entries of the same protein (UniProt P22290 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EZE 1.55 Å, Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to…
3RRC 1.95 Å, Crystal Structure of Region II from Plasmodium vivax Duffy Binding Protein
4NUU 1.95 Å, Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP)…
4YFS 2.1 Å, Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for…
8A44 2.49 Å, Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and…
4NUV 2.6 Å, Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein…
6OAN 2.9 Å, Structure of DBP in complex with human neutralizing antibody 053054
6R2S 3.04 Å, The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody…
6OAO 3.5 Å, Structure of DBP in complex with human neutralizing antibody 092096

Browse structure collections

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