5TKK: HIV-1 fusion peptide residue 512-519

Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex with HIV-1 fusion peptide residue 512-519. Determined by X-ray diffraction at 1.55 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Human immunodeficiency virus 1, Mus musculus
Chains: 3
Atoms: 3,693
Mol. weight: 48.79 kDa
Released: 4 Apr 2018

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

Secondary structure: helices and β-sheets

5TKK contains 18 α-helices and 43 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	514-516	3

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	7	3
β-strand	45-52	8	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	3
β-strand	99-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	125-127	3
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-171	9	5
β-strand	174-184	11	5
β-strand	194-199	6	6
α-helix	200-202	3
β-strand	204-209	6	6
α-helix	211-214	4

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-155	3	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	191-197	7	11
α-helix	204	1
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 fusion peptide residue 512-519	A	protein	8	Human immunodeficiency virus 1	P04578 (AlphaFold model)
mouse antibody vFP5.01 heavy chain	H	protein	222	Mus musculus
mouse antibody vFP5.01 light chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>5TKK_1 HIV-1 fusion peptide residue 512-519 (chains A)
AVGIGAVF

Sequence of entity 2 (H), FASTA

>5TKK_2 mouse antibody vFP5.01 heavy chain (chains H)
DVQLQESGPGLVKPSQSLSLTCSVTGYSITRAYYWNWIRQFPGNKLEWMGYILYDGRSDY
NPSLKNRVSITRDTSKNQFFLKLNSVTAEDTARYYCTREGNYRAYWGQGTLVTVSAAKTT
APSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVPIKPC

Sequence of entity 3 (L), FASTA

>5TKK_3 mouse antibody vFP5.01 light chain (chains L)
DIVMTQSQKFMSTSVGDRVSITCKASQNVGSDVAWYQQKPGQSPKLLIYSASNRYTGVPD
RFTGSGSGTDFTLTINNMKSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Xu, K., Acharya, P., Kong, R. et al. Nat Med (2018) 24:857-867. DOI 10.1038/s41591-018-0042-6 · PubMed

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
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…
6BXQ 1.58 Å, Crystal Structure of HLA-B*57:01 with an HIV peptide RKV

Browse structure collections

About this viewer

MolViewer shows 5TKK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.