6L1Y: Gp120/CD4 with a non-canonical surface

structure of gp120/CD4 with a non-canonical surface. Determined by X-ray diffraction at 2.47 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 2.47 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 2
Atoms: 4,271
Mol. weight: 65 kDa
Ligands: NAG
Released: 20 May 2020

Explore 6L1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L1Y contains 15 α-helices and 50 β-strands across 2 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: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	74-76	3	2
α-helix	77-78	2
β-strand	83-85	3	1
β-strand	91-94	4	3
α-helix	95-97	3
α-helix	99-115	17
β-strand	120-122	3	4
β-strand	200-202	3	4
β-strand	215	1	5
β-strand	216-218	3	2
α-helix	219-220	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	5
β-strand	256	1	6
β-strand	259-261	3	6
β-strand	271-273	3	6
α-helix	283	1
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-352	18
β-strand	357-360	4	6
β-strand	366	1	7
α-helix	368-371	4
β-strand	373-377	5	6
β-strand	380-384	5	6
α-helix	387-389	3
β-strand	392-393	2	6
β-strand	412-420	9	6
β-strand	422-424	3	4
β-strand	431-433	3	4
α-helix	435-437	3
β-strand	442-455	14	6
β-strand	464-469	6	6
α-helix	474-482	9
β-strand	485-489	5	1

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	12-14	3	8
β-strand	17	1	9
β-strand	27-29	3	7
β-strand	35-40	6	7
β-strand	43-46	4	7
α-helix	52-54	3
β-strand	55-56	2	8
α-helix	59-61	3
β-strand	66	1	9
β-strand	69-71	3	8
α-helix	76-78	3
β-strand	80-85	6	7
β-strand	90-98	9	7
β-strand	99-102	4	10
β-strand	107-108	2	11
β-strand	115-119	5	10
β-strand	127-131	5	12
β-strand	137-140	4	12
β-strand	143-145	3	10
β-strand	155-162	8	12
β-strand	167-174	8	12
β-strand	175-176	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gp120	A	protein	392	Human immunodeficiency virus 1	G4XFJ5
T-cell surface glycoprotein CD4	C	protein	177	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6L1Y_1 gp120 (chains A)
MDRAKLLLLLLLLLLPQAQAVGNLWVTVYYGVPVWKGATTTLFCASDAKAYETEVHNVWA
THACVPADPNPQEMVLENVTENFNMWKNDMVNQMQEDVISLWDQSLKPCVKLTGGSAITQ
ACPKVTFDPIPIHYCTPAGYAILKCNDKIFNGTGPCHNVSTVQCTHGIKPVVSTQLLLNG
SLAEGEIIIRSENLTNNVKTIIVHLNQSVEIVCTRPGNGGDIRQAHCNISEDKWNETLQR
VSKKLAEHFQNKTIKFASSSGGDLEVTTHSFNCRGEFFYCNTSGLFNGAYTPNGTKSNSS
SIITIPCRIKQIINMWQEVGRAMYAPPIKGNITCKSNITGLLLVRDGGTEPNDTETFRPG
GGDMRNNWRSELYKYKVVEIKPLGVAPTTTKR

Sequence of entity 2 (C), FASTA

>6L1Y_2 T-cell surface glycoprotein CD4 (chains C)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (EPE) are not listed.

Primary citation

A non-canonical binding interface in the crystal structure of HIV-1 gp120 core in complex with CD4. Duan, L.W., Zhang, H., Zhao, M.T. et al. Sci Rep (2017) 7:46733-46733. DOI 10.1038/srep46733 · PubMed

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