5IQ9: 10E8v4 Fab

Crystal structure of 10E8v4 Fab in complex with an HIV-1 gp41 peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,343
Mol. weight: 103.96 kDa
Released: 20 Apr 2016

Explore 5IQ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IQ9 contains 31 α-helices and 89 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.

Chain A: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	33-39	7	2
β-strand	46-51	6	2
α-helix	52B-53	3
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	2
β-strand	100I-103	7	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-128	9	4
β-strand	136-145	10	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
α-helix	171	1
β-strand	176-184	9	4
α-helix	186-188	3
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
β-strand	9-14	5	7
β-strand	19-24	6	6
α-helix	26-29	4
β-strand	34-38	5	7
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-91	8	7
β-strand	96-98	3	7
β-strand	102-107	6	7
β-strand	112	1	9
α-helix	113-114	2
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
α-helix	156	1
β-strand	160-162	3	10
α-helix	163-165	3
β-strand	166-167	2	10
β-strand	173-181	9	10
α-helix	183-188	6
β-strand	192-198	7	11
β-strand	201-207	7	11

Chains C and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	672-683	12

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
β-strand	33-39	7	13
β-strand	46-51	6	13
α-helix	52B-53	3
β-strand	57-59	3	13
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-98	11	13
β-strand	100I-103	7	13
β-strand	107-111	5	13
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-128	9	15
β-strand	136-145	10	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	159	1	16
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-184	9	15
α-helix	186-188	3
β-strand	194-200	7	16
β-strand	205-211	7	16

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	17
β-strand	9-13	4	18
β-strand	19-24	6	17
α-helix	26-29	4
β-strand	34-38	5	18
β-strand	45-48	4	18
β-strand	49	1	19
β-strand	53	1	19
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-91	8	18
β-strand	96-98	3	18
β-strand	102-106	5	18
β-strand	112	1	20
α-helix	113-114	2
β-strand	115-119	5	21
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	21
β-strand	141	1	20
β-strand	146-151	6	22
β-strand	154-155	2	22
α-helix	156	1
β-strand	160-162	3	21
β-strand	166-167	2	21
β-strand	173-181	9	21
α-helix	183-186	4
β-strand	192-198	7	22
β-strand	201-207	7	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
10E8v4 Heavy Chain	A, H	protein	232	Homo sapiens	P01857 (AlphaFold model)
10E8v4 Light Chain	B, L	protein	210	Homo sapiens	P0DOY2 (AlphaFold model)
gp41 MPER peptide	C, P	protein	33	Human immunodeficiency virus 1	Q1HSF8

Sequence of entity 1 (A, H), FASTA

>5IQ9_1 10E8v4 Heavy Chain (chains A, H)
EVRLVESGGGLVKPGGSLRLSCSASGFDFDNAWMTWVRQPPGKGLEWVGRITGPGEGWSV
DYAESVKGRFTISRDNTKNTLYLEMNNVRTEDTGYYFCARTGKYYDFWSGYPPGEEYFQD
WGQGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 2 (B, L), FASTA

>5IQ9_2 10E8v4 Light Chain (chains B, L)
SELTQDPAVSVALKQTVTITCRGDSLRSHYASWYQKKPGQAPVLLFYGKNNRPSGIPDRF
SGSASGNRASLTITGAQAEDEADYYCSSRDKSGSRLSVFGGGTKLTVLSQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAP

Sequence of entity 3 (C, P), FASTA

>5IQ9_3 gp41 MPER peptide (chains C, P)
RRRNEQELLELDKWASLWNWFDITNWLWYIRRR

Primary citation

Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design. Kwon, Y.D., Georgiev, I.S., Ofek, G. et al. J Virol (2016) 90:5899-5914. DOI 10.1128/JVI.03246-15 · PubMed

Other PDB entries of the same protein (UniProt P01857 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
5HSF 1.52 Å, 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
1L6X 1.65 Å, Fc fragment of rituximab bound to a minimized version of the B-domain from protein A…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
5JIH 1.66 Å, Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)
3MCL 1.7 Å, Anti-beta-amyloid antibody c706 fab in space group P21
5U66 1.7 Å, Modified single helix from the B-domain of protein A bound to IgG1 Fc
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

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