6OAO: DBP

Structure of DBP in complex with human neutralizing antibody 092096. Determined by X-ray diffraction at 3.5 Å resolution. Released 12 Jun 2019.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Plasmodium vivax, Homo sapiens
Chains: 12
Atoms: 24,648
Mol. weight: 382.28 kDa
Released: 12 Jun 2019

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

Secondary structure: helices and β-sheets

6OAO contains 132 α-helices and 164 β-strands across 12 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: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	221-222	2
β-strand	229	1	1
β-strand	238	1	1
α-helix	240-244	5
α-helix	248-251	4
α-helix	265-266	2
α-helix	267-272	6
α-helix	273-290	18
α-helix	297-314	18
α-helix	324-333	10
α-helix	340-361	22
α-helix	363-368	6
α-helix	379-382	4
α-helix	388-415	28
β-strand	418	1	2
β-strand	424	1	2
α-helix	425-427	3
α-helix	430-464	35
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	3
β-strand	14-15	2	4
β-strand	22-29	8	3
α-helix	33-35	3
β-strand	39-43	5	4
β-strand	49-54	6	4
β-strand	63-64	2	4
α-helix	66-68	3
β-strand	72-77	6	3
β-strand	82-87	6	3
α-helix	92-94	3
β-strand	96-102	7	4
β-strand	114-115	2	4
β-strand	119-122	4	4
β-strand	148	1	5
β-strand	149-150	2	6
β-strand	161-167	7	6
α-helix	170-174	5
β-strand	178-183	6	7
β-strand	190-193	4	7
β-strand	194	1	8
β-strand	198	1	8
β-strand	207-212	6	6
β-strand	215-221	7	6
β-strand	230-237	8	7
β-strand	242-245	4	7
β-strand	246	1	5
β-strand	250	1	7

Chain C: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	221-222	2
β-strand	229	1	9
β-strand	238	1	9
α-helix	240-244	5
α-helix	248-251	4
α-helix	265-266	2
α-helix	267-271	5
α-helix	272-290	19
α-helix	297-314	18
α-helix	324-333	10
α-helix	340-361	22
α-helix	363-367	5
α-helix	379-382	4
α-helix	388-415	28
β-strand	418	1	10
β-strand	424	1	10
α-helix	425-427	3
α-helix	430-463	34
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Chain D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	11
α-helix	11-13	3
β-strand	14-15	2	12
β-strand	22-29	8	11
α-helix	33-35	3
β-strand	39-43	5	12
β-strand	49-56	8	12
β-strand	60-64	5	12
α-helix	66-68	3
β-strand	72-77	6	11
β-strand	82-87	6	11
α-helix	92-94	3
β-strand	96-102	7	12
β-strand	114-115	2	12
β-strand	119-122	4	12
β-strand	149-150	2	13
β-strand	162-167	6	13
α-helix	170-174	5
β-strand	178-183	6	14
β-strand	191-193	3	14
β-strand	194	1	15
β-strand	198	1	15
β-strand	207-212	6	13
β-strand	215-220	6	13
α-helix	225-227	3
β-strand	230-237	8	14
β-strand	242-245	4	14
β-strand	249-250	2	14

Chain E: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	221-222	2
β-strand	229	1	16
β-strand	238	1	16
α-helix	240-244	5
α-helix	248-251	4
α-helix	265-266	2
α-helix	267-272	6
α-helix	273-290	18
α-helix	297-314	18
α-helix	324-336	13
α-helix	340-361	22
α-helix	363-367	5
α-helix	388-415	28
β-strand	418	1	17
β-strand	424	1	17
α-helix	425-427	3
α-helix	430-463	34
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Chain F: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	18
β-strand	14-16	3	19
β-strand	22-29	8	18
α-helix	33-35	3
β-strand	39-43	5	19
β-strand	49-54	6	19
β-strand	63-64	2	19
α-helix	66-68	3
β-strand	72-77	6	18
β-strand	82-87	6	18
α-helix	92-94	3
β-strand	96-102	7	19
β-strand	114-115	2	19
β-strand	119-123	5	19
β-strand	149-150	2	20
β-strand	162-167	6	20
α-helix	170-174	5
β-strand	178-183	6	21
β-strand	190-193	4	21
β-strand	194	1	22
β-strand	198	1	22
β-strand	207-212	6	20
β-strand	215-220	6	20
β-strand	230-237	8	21
β-strand	242-245	4	21
β-strand	249-250	2	21

Chain G: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	217	1	23
β-strand	219	1	23
α-helix	221-222	2
β-strand	229	1	24
β-strand	238	1	24
α-helix	240-244	5
α-helix	248-251	4
α-helix	265-266	2
α-helix	267-272	6
α-helix	273-290	18
α-helix	297-314	18
α-helix	324-336	13
α-helix	340-351	12
α-helix	354-361	8
α-helix	363-367	5
α-helix	379-382	4
α-helix	388-415	28
β-strand	418	1	25
β-strand	424	1	25
α-helix	425-427	3
α-helix	430-463	34
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	26
β-strand	14-15	2	27
β-strand	22-29	8	26
α-helix	33-35	3
β-strand	39-43	5	27
β-strand	49-54	6	27
β-strand	63-64	2	27
α-helix	66-68	3
β-strand	72-77	6	26
β-strand	82-87	6	26
α-helix	92-94	3
β-strand	96-102	7	27
β-strand	114-115	2	27
β-strand	119-122	4	27
β-strand	148	1	28
β-strand	149-150	2	29
β-strand	162-167	6	29
α-helix	170-174	5
β-strand	178-183	6	30
β-strand	190-193	4	30
β-strand	194	1	31
β-strand	198	1	31
β-strand	207-212	6	29
β-strand	215-220	6	29
α-helix	225-227	3
β-strand	230-237	8	30
β-strand	242-245	4	30
β-strand	246	1	28
β-strand	249-250	2	30

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Duffy binding surface protein region II	A, C, E, G, I, K	protein	315	Plasmodium vivax	P22290 (AlphaFold model)
Antibody 092096 single chain variable fragment	B, D, F, H, J, L	protein	251	Homo sapiens

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>6OAO_1 Duffy binding surface protein region II (chains A, C, E, G, I, K)
NTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFRKL
YLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVEN
NLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQIY
RWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQW
DVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVE
EAKKNTQEVVTNVDN

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>6OAO_2 Antibody 092096 single chain variable fragment (chains B, D, F, H, J, L)
MVHSQVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDREDG
ESIYAQKFQGRVTLTEDTSTDSVYMELSNLRSDDTAVYFCATDFGGSYFYAFDIWGQGTM
VTVSSGGGGSGGGGSGGGGSQSVLTQSPSASGTPGQRVTISCSGSSSNIGRNPVNWFQHL
PGTAPQLLIYSNDQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCEAWDDSLNGVV
FGGGTKLTVLG

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…
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…
5F3J 4.0 Å, Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10

Browse structure collections

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