5N88: Antibody

Crystal structure of antibody bound to viral protein. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,581
Mol. weight: 46.42 kDa
Released: 20 Dec 2017

Explore 5N88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N88 contains 21 α-helices and 27 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-12	2	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	5
α-helix	74-76	3
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	106-108	3
β-strand	110	1	4
α-helix	111-113	3
β-strand	116-117	2	7
β-strand	121-123	3	7
β-strand	124-125	2	6

Chain D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	348-362	15
β-strand	364	1	4
α-helix	370-382	13
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-424	15

Chain E: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	347-362	16
β-strand	364	1	3
α-helix	370-382	13
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-423	14

Chain H: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	106-108	3
β-strand	110	1	3
α-helix	111-113	3
β-strand	114-117	4	2
β-strand	121-125	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VH59 antibody	A, H	protein	126	Homo sapiens
PC4 and SFRS1-interacting protein	D	protein	79	Homo sapiens	O75475 (AlphaFold model)
PC4 and SFRS1-interacting protein	E	protein	80	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5N88_1 VH59 antibody (chains A, H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSTFSMNWVRQAPGKGLEWVSYISRTSKTIYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGGWALGDEIPSSFLEFDYWGQG
TLVTVS

Sequence of entity 2 (D), FASTA

>5N88_2 PC4 and SFRS1-interacting protein (chains D)
SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRF
KVSQVIMEKSTMLYNKFKN

Sequence of entity 3 (E), FASTA

>5N88_3 PC4 and SFRS1-interacting protein (chains E)
GSSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIR
RFKVSQVIMEKSTMLYNKFK

Primary citation

Intracellular immunization against HIV infection with an intracellular antibody that mimics HIV integrase binding to the cellular LEDGF protein. Bao, L., Hannon, C., Cruz-Mignoni, A. et al. Sci Rep (2017) 7:16869-16869. DOI 10.1038/s41598-017-16742-2 · PubMed

Other PDB entries of the same protein (UniProt O75475 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRJ 1.3 Å, LEDGF/p75 IBD dimer
9S81 1.63 Å, Crystal structure of the LEDGF PWWP domain
2B4J 2.02 Å, Structural basis for the recognition between HIV-1 integrase and LEDGF/p75
5OYM 2.05 Å, HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor
4FU6 2.1 Å, Crystal structure of the PSIP1 PWWP domain
9S83 2.1 Å, Crystal structure of de novo designed binder JUBO4 and the LEDGF PWWP domain
3HPH 2.64 Å, Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
8PEO 2.69 Å, H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex
9S28 2.8 Å, MVV STC intasome in complex with LEDGF
9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
3U88 3.0 Å, Crystal structure of human menin in complex with MLL1 and LEDGF
7OUF 3.0 Å, Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450

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