1N0X: Broadly Neutralizing Anti-HIV-1 Antibody

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope. Determined by X-ray diffraction at 1.8 Å resolution. Released 13 Apr 2004.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,899
Mol. weight: 103.77 kDa
Ligands: CXS
Released: 13 Apr 2004

Explore 1N0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N0X contains 34 α-helices and 91 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 H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	57-59	3	2
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	117	1	7
β-strand	120-124	5	8
β-strand	138-147	10	8
β-strand	148	1	7
β-strand	153-157	4	9
α-helix	162-164	3
β-strand	166	1	9
β-strand	171-173	3	8
α-helix	174-176	3
β-strand	177-178	2	8
β-strand	185-193	9	8
α-helix	195-197	3
β-strand	207-212	6	9
α-helix	213-215	3
β-strand	217-222	6	9

Chain K: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
α-helix	7-9	3
β-strand	10-12	3	11
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	57-59	3	11
α-helix	61-63	3
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-94	7	11
α-helix	100C	1
β-strand	102-103	2	11
β-strand	107-111	5	11
β-strand	117	1	16
α-helix	118-119	2
β-strand	120-124	5	17
β-strand	137-147	11	17
β-strand	148	1	16
β-strand	153-157	4	18
α-helix	162-164	3
β-strand	166	1	18
β-strand	171-173	3	17
α-helix	174-176	3
β-strand	177-178	2	17
β-strand	185-194	10	17
α-helix	195-197	3
β-strand	207-212	6	18
α-helix	213-215	3
β-strand	217-222	6	18

Chain L: 8 helices, 21 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	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
β-strand	98	1	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain M: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	11
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-154	2	14
α-helix	155	1
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-187	5
β-strand	191-197	7	14
β-strand	205-210	6	14

Chain P: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	19
β-strand	13-16	4	19

Chain R: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	20
β-strand	13-16	4	20
β-strand	19	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin light chain	L, M	protein	215	Homo sapiens	P01834 (AlphaFold model)
Immunoglobulin heavy chain	H, K	protein	230	Homo sapiens	P0DOX5 (AlphaFold model)
B2.1 peptide	P, R	protein	21	synthetic construct

Sequence of entity 1 (L, M), FASTA

>1N0X_1 IMMUNOGLOBULIN LIGHT CHAIN (chains L, M)
EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGIS
DRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Sequence of entity 2 (H, K), FASTA

>1N0X_2 IMMUNOGLOBULIN HEAVY CHAIN (chains H, K)
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEF
SAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKG
TTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (P, R), FASTA

>1N0X_3 B2.1 peptide (chains P, R)
HERSYMFSDLENRCIAAEAKK

Ligands and cofactors

ID	Name	Formula	Copies
CXS	3-cyclohexyl-1-propylsulfonic acid	C9 H19 N O3 S	1

Water and common crystallization additives (K, SO4, GOL) are not listed.

Primary citation

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope. Saphire, E.O., Montero, M., Menendez, A. et al. To be published.

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
6B9Z 1.82 Å, Trastuzumab Fab v3
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1
1GAF 1.95 Å, 48G7 hybridoma line FAB complexed with hapten 5-(para-nitrophenyl phosphonate)-pentanoic…

Browse structure collections

About this viewer

MolViewer shows 1N0X 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.