2NY7: HIV-1 gp120 Envelope Glycoprotein

HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12. Determined by X-ray diffraction at 2.3 Å resolution. Released 6 Feb 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,181
Mol. weight: 86.62 kDa
Ligands: NAG
Released: 6 Feb 2007

Explore 2NY7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NY7 contains 29 α-helices and 69 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 G: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	85	1	1
β-strand	91-94	4	2
α-helix	108-110	3
β-strand	112-114	3	3
β-strand	210-212	3	3
α-helix	213-214	2
β-strand	215	1	4
β-strand	218	1	5
α-helix	219-220	2
β-strand	223-228	6	1
β-strand	236-239	4	2
β-strand	242-245	4	1
β-strand	247	1	5
α-helix	248-250	3
β-strand	251	1	4
β-strand	256	1	6
β-strand	259-261	3	7
α-helix	264-266	3
β-strand	271-273	3	7
α-helix	283	1
β-strand	284-297	14	7
β-strand	330-334	5	7
α-helix	335-353	19
β-strand	358-361	4	7
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	388-390	3
β-strand	393-395	3	7
β-strand	413-417	5	7
β-strand	418-427	10	6
β-strand	432-436	5	6
β-strand	445-456	12	7
β-strand	465-470	6	7
α-helix	477-480	4
β-strand	486-490	5	1

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
α-helix	44	1
β-strand	45-51	7	9
β-strand	57-59	3	9
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-94	7	9
α-helix	100C	1
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	133-134	2	11
β-strand	137-147	11	11
β-strand	148	1	10
β-strand	153-157	4	12
α-helix	162-164	3
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-178	2	11
β-strand	185-194	10	11
α-helix	195-197	3
β-strand	206-212	7	12
α-helix	213-215	3
β-strand	217-225	7	12

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	144-150	7	17
β-strand	153-154	2	17
α-helix	155	1
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-198	8	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP120	G	protein	317	Human immunodeficiency virus 1	P35961
Antibody b12, heavy chain	H	protein	230	Homo sapiens
Antibody b12, light chain	L	protein	215	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>2NY7_1 ENVELOPE GLYCOPROTEIN GP120 (chains G)
EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCVKLTPLCVGAGSCNTSVITQACP
KVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLA
EEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGAGHCNIARAKWNNTLKQIASKLREQFGN
NKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTIT
LPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDM
RDNWRSELYKYKVVKIE

Sequence of entity 2 (H), FASTA

>2NY7_2 ANTIBODY b12, HEAVY CHAIN (chains H)
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEF
SAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKG
TTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC

Sequence of entity 3 (L), FASTA

>2NY7_3 ANTIBODY b12, LIGHT CHAIN (chains L)
EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGIS
DRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13

Primary citation

Structural definition of a conserved neutralization epitope on HIV-1 gp120. Zhou, T., Xu, L., Dey, B. et al. Nature (2007) 445:732-737. DOI 10.1038/nature05580 · PubMed

Other PDB entries of the same protein (UniProt P35961), best resolution first:

4JZZ 1.49 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4JZW 1.78 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4KA2 1.79 Å, Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
4RWY 2.13 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131…
4K0A 2.13 Å, Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120
4LAJ 2.14 Å, Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic…
1YYM 2.2 Å, crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120…
2I60 2.4 Å, Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1…
4DVR 2.5 Å, Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
4JO3 2.6 Å, Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus…
1YYL 2.75 Å, crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

Browse structure collections

About this viewer

MolViewer shows 2NY7 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.