6PDR: Antibody vFP25.18 light chain

Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion peptide (residue 512-519). Determined by X-ray diffraction at 1.55 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,837
Mol. weight: 48.21 kDa
Released: 24 Jun 2020

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

Secondary structure: helices and β-sheets

6PDR contains 14 α-helices and 44 β-strands across 3 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: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	513	1	2

Chain H: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	10-12	3	2
β-strand	18-26	9	7
β-strand	32-39	8	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	101-103	3	2
β-strand	107-111	5	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
α-helix	129-131	3
β-strand	135-145	11	9
β-strand	146	1	8
α-helix	149-150	2
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	163-171	9	9
β-strand	174-184	11	9
β-strand	194-199	6	10
α-helix	200-202	3
β-strand	204-209	6	10

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	31	1	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	4
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	191-197	7	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody vFP25.18 light chain	L	protein	219	Mus musculus
antibody vFP25.18 heavy chain	H	protein	218	Mus musculus
HIV fusion peptide residue 512-519	A	protein	8	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6PDR_1 antibody vFP25.18 light chain (chains L)
DVLMTQSPLSLPVSLGDQASISCRSSQSILHSNGNTYLDWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCFQGSHVPLTFGSGTKLEIKRTDAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>6PDR_2 antibody vFP25.18 heavy chain (chains H)
EFQLQQSGPELVKPGASVKISCKASGDSFTDYNLSWVKQINGKSLEWIGVINPNYGTTTY
NQKFKAKATLTVDQSSSTAYMQLNSLTSEDSAVYYCAFSSRLFGYWGQGTTLTVSSASTT
PPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (A), FASTA

>6PDR_3 HIV fusion peptide residue 512-519 (chains A)
AVGIGAVF

Primary citation

Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies. Xu, K., Liu, K., Wang, Y. et al. To be published.

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6BXQ 1.58 Å, Crystal Structure of HLA-B*57:01 with an HIV peptide RKV

Browse structure collections

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