9EZE: Duffy receptor

Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9. Determined by X-ray diffraction at 1.55 Å resolution. Released 29 Oct 2025.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Plasmodium vivax Sal-1, Homo sapiens
Chains: 6
Atoms: 9,514
Mol. weight: 181.13 kDa
Released: 29 Oct 2025

Explore 9EZE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EZE contains 50 α-helices and 88 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.

Chains A and D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	387-415	29
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

Chains B and E: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	1
β-strand	30-31	2	2
β-strand	37-44	8	1
β-strand	54-60	7	3
β-strand	67-72	6	3
β-strand	78-80	3	3
β-strand	88-93	6	1
α-helix	94-96	3
β-strand	98-103	6	1
α-helix	108-110	3
β-strand	112-120	9	3
β-strand	123-127	5	3
β-strand	131-133	3	3
β-strand	134-135	2	2
α-helix	139-140	2
β-strand	141	1	4
α-helix	142-143	2
β-strand	144-148	5	5
α-helix	149-151	3
α-helix	154-155	2
β-strand	159-169	11	5
β-strand	170	1	4
β-strand	175-178	4	6
α-helix	179-181	3
β-strand	183	1	6
β-strand	187-189	3	5
α-helix	190-192	3
β-strand	193-194	2	5
β-strand	200-209	10	5
α-helix	210-212	3
β-strand	219-224	6	6
α-helix	225-227	3
β-strand	229-234	6	6

Chains C and F: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	7
β-strand	29-33	5	8
β-strand	38-44	7	7
β-strand	52-57	6	8
β-strand	64-68	5	8
β-strand	72-73	2	8
α-helix	74	1
β-strand	81-86	6	7
β-strand	89-94	6	7
α-helix	99-101	3
β-strand	103-109	7	8
α-helix	115	1
β-strand	116-117	2	8
β-strand	121-126	6	8
β-strand	130	1	9
α-helix	131-132	2
β-strand	133-137	5	10
α-helix	138-140	3
α-helix	141-144	4
β-strand	148-158	11	10
β-strand	159	1	9
β-strand	164-169	6	11
β-strand	172-173	2	11
α-helix	174	1
β-strand	178-182	5	10
α-helix	183-186	4
β-strand	192-201	10	10
α-helix	202-206	5
β-strand	210-216	7	11
β-strand	224-229	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Duffy receptor	A, D	protein	300	Plasmodium vivax Sal-1	P22290 (AlphaFold model)
Antibody DB9 heavy chain	B, E	protein	278	Homo sapiens
Antibody DB9 light chain	C, F	protein	233	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>9EZE_1 Duffy receptor (chains A, D)
SGNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFR
KLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVV
ENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQ
IYRWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKN
QWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS

Sequence of entity 2 (B, E), FASTA

>9EZE_2 Antibody DB9 heavy chain (chains B, E)
HPLCLSLHRCPLPGPTAPRFYRLNSTMGWSCIILFLVATATGVHSEVQLQESGPGLVKPS
ETLSLTCTVSGGSVSSSTYYWGWVRQPPGKGLEWIGSIYYSGSTYYNPSLKSRVTISVDT
SKNQFSLKLSSVTAADTAVYYCARDGTGALDLWGRGTLVTVSSASTKGPSVFPLAPSSKS
TSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLG
TQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPDPST

Sequence of entity 3 (C, F), FASTA

>9EZE_3 Antibody DB9 light chain (chains C, F)
MGWSCIILFLVATATGVHGDIVMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQRPG
KAPRLLIYKASSLLSGVPSRFGGSGSGTDFTLTISSLQPDDFATYHCQHYNTYPWTFGQG
TKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Subdomain 3 of the Plasmodium vivax Duffy binding protein as a vaccine candidate. Barber, N.M., Higgins, M.K. To be published.

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

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

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