2NY1: HIV-1 gp120 Envelope Glycoprotein

HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4 and Antibody 17b. Determined by X-ray diffraction at 1.99 Å resolution. Released 6 Feb 2007.

Method: X-ray diffraction
Resolution: 1.99 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 4
Atoms: 7,852
Mol. weight: 106.81 kDa
Ligands: NAG
Released: 6 Feb 2007

Explore 2NY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NY1 contains 33 α-helices and 89 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: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	84-85	2	1
β-strand	91-94	4	2
α-helix	99-115	17
β-strand	120-123	4	3
β-strand	199-202	4	3
α-helix	212-214	3
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	259-261	3	6
α-helix	264-266	3
β-strand	271-273	3	6
β-strand	284-297	14	6
β-strand	330-334	5	6
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	6
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	8
β-strand	381-385	5	8
β-strand	393-395	3	6
β-strand	413-417	5	6
β-strand	418-421	4	8
β-strand	423-425	3	3
β-strand	432-434	3	3
α-helix	436-438	3
β-strand	444-456	13	6
β-strand	465-470	6	6
α-helix	475-483	9
β-strand	486-490	5	1

Chain B: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1003-1007	5	7
β-strand	1012-1014	3	9
β-strand	1017	1	10
β-strand	1026-1030	5	7
β-strand	1035-1040	6	7
β-strand	1043-1046	4	7
α-helix	1052-1054	3
β-strand	1055-1056	2	9
α-helix	1059-1064	6
β-strand	1066	1	10
β-strand	1069-1071	3	9
α-helix	1076-1078	3
β-strand	1080-1086	7	7
β-strand	1089-1098	10	7
β-strand	1099-1102	4	11
β-strand	1107-1109	3	12
β-strand	1114-1119	6	11
β-strand	1127-1131	5	13
β-strand	1137-1140	4	13
β-strand	1143-1146	4	11
α-helix	1151-1153	3
β-strand	1155-1163	9	13
β-strand	1166-1174	9	13
β-strand	1175-1177	3	12

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2002-2003	2
β-strand	2004-2007	4	14
β-strand	2010-2013	4	15
β-strand	2019-2025	7	14
β-strand	2033-2038	6	15
β-strand	2045-2049	5	15
β-strand	2053-2054	2	15
α-helix	2055	1
β-strand	2062-2067	6	14
β-strand	2070-2075	6	14
α-helix	2080-2082	3
β-strand	2085-2090	6	15
β-strand	2099-2100	2	15
β-strand	2104-2108	5	15
β-strand	2113	1	16
α-helix	2114-2115	2
β-strand	2116-2120	5	17
α-helix	2121-2123	3
α-helix	2124-2127	4
β-strand	2131-2141	11	17
β-strand	2142	1	16
β-strand	2147-2152	6	18
β-strand	2155-2156	2	18
α-helix	2157	1
β-strand	2161-2165	5	17
α-helix	2166-2169	4
β-strand	2175-2184	10	17
α-helix	2185-2188	4
β-strand	2193-2199	7	18
β-strand	2207-2212	6	18

Chain D: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3003-3006	4	19
α-helix	3007-3009	3
β-strand	3010-3012	3	20
β-strand	3018-3025	8	19
α-helix	3029-3031	3
β-strand	3032-3039	8	20
β-strand	3045-3052	8	20
β-strand	3057-3060	4	20
β-strand	3068-3073	6	19
β-strand	3078-3083	6	19
α-helix	3088-3090	3
β-strand	3092-3100	9	20
α-helix	3104-3106	3
β-strand	3117-3118	2	20
β-strand	3122-3126	5	20
α-helix	3129-3131	3
β-strand	3132	1	21
α-helix	3133-3134	2
β-strand	3135-3139	5	22
β-strand	3150-3160	11	22
β-strand	3161	1	21
β-strand	3166-3169	4	23
α-helix	3170-3172	3
β-strand	3178-3180	3	22
α-helix	3181-3183	3
β-strand	3184-3185	2	22
β-strand	3191-3200	10	22
α-helix	3201-3203	3
β-strand	3210-3215	6	23
α-helix	3216-3218	3
β-strand	3220-3225	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP120	A	protein	317	Human immunodeficiency virus 1	Q993A8
T-cell surface glycoprotein CD4	B	protein	184	Homo sapiens	P01730 (AlphaFold model)
Antibody 17B, light chain	C	protein	214	Homo sapiens	Q6P5S8 (AlphaFold model)
Antibody 17B, heavy chain	D	protein	229	Homo sapiens	Q6N030 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NY1_1 ENVELOPE GLYCOPROTEIN GP120 (chains A)
EVVLVNVTENFNMWKNDMVEQMHEDICSLWDQSLKPCVKLTPLCVGAGSCNTSVITQACP
KVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLA
EEEVVIRSVNFTDNAKTIIVQLNTSVEINCTGAGHCNIARAKWNNTLKQIASKLREQFGN
NKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTIT
LPCRIKQIINMWCKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDM
RDNWRSELYKYKVVKIE

Sequence of entity 2 (B), FASTA

>2NY1_2 T-cell surface glycoprotein CD4 (chains B)
MKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRR
SLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLE
SPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAF
QKAS

Sequence of entity 3 (C), FASTA

>2NY1_3 ANTIBODY 17B, LIGHT CHAIN (chains C)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 4 (D), FASTA

>2NY1_4 ANTIBODY 17B, HEAVY CHAIN (chains D)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

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 Q993A8), best resolution first:

2NY3 2.0 Å, HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4…

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