6OAN: DBP

Structure of DBP in complex with human neutralizing antibody 053054. Determined by X-ray diffraction at 2.9 Å resolution. Released 12 Jun 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Plasmodium vivax, Homo sapiens
Chains: 4
Atoms: 7,744
Mol. weight: 130.92 kDa
Released: 12 Jun 2019

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

Secondary structure: helices and β-sheets

6OAN contains 34 α-helices and 54 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	229	1	1
β-strand	238	1	1
α-helix	240-243	4
α-helix	248-251	4
α-helix	265-290	26
α-helix	297-315	19
α-helix	324-336	13
α-helix	342-361	20
α-helix	363-368	6
α-helix	372-374	3
α-helix	379-383	5
α-helix	388-412	25
α-helix	433-462	30
α-helix	474-481	8
α-helix	487-494	8

Chain B: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	2
β-strand	10-11	2	3
β-strand	15	1	4
β-strand	22-27	6	3
β-strand	29	1	2
β-strand	38-45	8	5
β-strand	52-57	6	5
β-strand	63-65	3	5
α-helix	67-72	6
β-strand	73-78	6	3
α-helix	79-81	3
β-strand	83-88	6	3
α-helix	93-95	3
β-strand	97-105	9	5
β-strand	113-116	4	5
β-strand	120-122	3	5
β-strand	123	1	4
β-strand	150	1	6
β-strand	154-157	4	7
β-strand	163-168	6	6
α-helix	172-174	3
β-strand	178-182	5	7
β-strand	189-192	4	7
β-strand	193	1	8
β-strand	197	1	8
β-strand	206-211	6	6
β-strand	214-219	6	6
α-helix	224-226	3
β-strand	228-236	9	7
β-strand	241-244	4	7
β-strand	248-252	5	7

Chain C: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	229	1	9
β-strand	238	1	9
α-helix	240-243	4
α-helix	248-251	4
α-helix	267-290	24
α-helix	297-315	19
α-helix	324-336	13
α-helix	342-361	20
α-helix	363-368	6
α-helix	379-383	5
α-helix	388-409	22
α-helix	433-462	30
α-helix	474-481	8
α-helix	487-494	8

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
β-strand	15-16	2	11
β-strand	22-29	8	10
β-strand	38-45	8	12
β-strand	52-57	6	12
β-strand	63-65	3	12
α-helix	67-72	6
β-strand	73-78	6	10
β-strand	83-88	6	10
α-helix	93-95	3
β-strand	97-105	9	12
β-strand	113-116	4	12
β-strand	120-122	3	12
β-strand	123-124	2	11
β-strand	150	1	13
β-strand	154-157	4	14
β-strand	163-168	6	13
α-helix	172-174	3
β-strand	178-182	5	14
β-strand	189-192	4	14
β-strand	193	1	15
β-strand	197	1	15
β-strand	206-211	6	13
β-strand	214-219	6	13
α-helix	224-226	3
β-strand	228-236	9	14
β-strand	241-244	4	14
β-strand	248-252	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Duffy binding surface protein region II	A, C	protein	315	Plasmodium vivax	P22290 (AlphaFold model)
Antibody 053054 single chain variable fragment	B, D	protein	266	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6OAN_1 Duffy binding surface protein region II (chains A, C)
NTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFRKL
YLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVEN
NLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQIY
RWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQW
DVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVE
EAKKNTQEVVTNVDN

Sequence of entity 2 (B, D), FASTA

>6OAN_2 Antibody 053054 single chain variable fragment (chains B, D)
MVHSQVQLQESGPGLVKPSQTLSLTCNVSGDSINSGDYYWIWIRQPPGKGLEWIGNIYYS
GTAYYNPSLKTRLIISIDTSTNQFSLKVTSVTAADTAIYYCARASTTVVSPWLDPWGQGT
LVTVSSAGGGGSGGGGSGGGGSSVTSYELTQPSSVAVAPGQTARIPCGGDNIESKGVHWY
QQKPGQAPVLVVYDDHDRPSGIPERFSGSNSGNTATLTVSRVEAGDEADYYCQVWDTSSE
HPVFGGGTKLTVLGQPKAAPSVTLFP

Primary citation

Structural basis for neutralization of Plasmodium vivax by naturally acquired human antibodies that target DBP. Urusova, D., Carias, L., Huang, Y. et al. Nat Microbiol (2019) 4:1486-1496. DOI 10.1038/s41564-019-0461-2 · 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…
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
5F3J 4.0 Å, Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10

Browse structure collections

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