4DKO: Clade A/E 93TH057 HIV-1 gp120 core

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224. Determined by X-ray diffraction at 1.98 Å resolution. Released 2 May 2012.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
Chains: 2
Atoms: 6,090
Mol. weight: 84.4 kDa
Ligands: NAG, 0LM
Released: 2 May 2012

Explore 4DKO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DKO contains 26 α-helices and 56 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77-78	2
β-strand	83-85	3	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	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
α-helix	264-266	3
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
α-helix	357	1
β-strand	358-361	4	6
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	413-420	8	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	435-439	5
β-strand	443-456	14	6
α-helix	457	1
β-strand	465-470	6	6
α-helix	476-483	8
β-strand	486-491	6	1

Chain C: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	7
β-strand	53-56	4	8
α-helix	65-73	9
β-strand	74-76	3	8
α-helix	77-78	2
β-strand	84-85	2	7
β-strand	91-94	4	9
α-helix	95-97	3
α-helix	99-115	17
β-strand	120-123	4	10
β-strand	199-202	4	10
β-strand	215	1	11
β-strand	216-218	3	8
β-strand	223-228	6	7
β-strand	236-239	4	9
β-strand	242-245	4	7
β-strand	247	1	8
β-strand	251	1	11
β-strand	256	1	12
β-strand	259-261	3	12
α-helix	264-266	3
α-helix	270	1
β-strand	271-273	3	12
α-helix	283	1
β-strand	284-298	15	12
β-strand	328-334	7	12
α-helix	335-350	16
α-helix	357-358	2
β-strand	359-361	3	12
α-helix	369-372	4
β-strand	374-378	5	12
β-strand	381-385	5	12
α-helix	388-391	4
β-strand	413-420	8	12
β-strand	423-425	3	10
β-strand	431-434	4	10
α-helix	436-439	4
β-strand	443-456	14	12
α-helix	457	1
β-strand	466-470	5	12
α-helix	476-483	8
β-strand	486-491	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 gp120 core	A, C	protein	353	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1	Q0ED31

Sequence of entity 1 (A, C), FASTA

>4DKO_1 HIV-1 gp120 core (chains A, C)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	22
0LM	N-(4-chloro-3-fluorophenyl)-N'-(1,2,2,6,6-pentamethylpiperidin-4-yl)ethanediami…	C18 H25 Cl F N3 O2	2

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

Primary citation

Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors. Lalonde, J.M., Kwon, Y.D., Jones, D.M. et al. J Med Chem (2012) 55:4382-4396. DOI 10.1021/jm300265j · PubMed

Other PDB entries of the same protein (UniProt Q0ED31), best resolution first:

4XVT 1.69 Å, Crystal structure of HIV-1 93TH057 coreE gp120 with antibody…
4DKP 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50
4DKR 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169
4YDL 1.8 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex…
4H8W 1.85 Å, Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with…
4DKQ 1.89 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228
3SE8 1.9 Å, Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with…
3TGT 1.9 Å, Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
3SE9 2.0 Å, Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with…
4YDK 2.05 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex…
4OLZ 2.1 Å, Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120…
4OM1 2.13 Å, Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057…

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