1VRT: HIV-1 rt from four rt-inhibitor complexes

High resolution structures of HIV-1 rt from four rt-inhibitor complexes. Determined by X-ray diffraction at 2.2 Å resolution. Released 3 Apr 1996.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 7,953
Mol. weight: 116.28 kDa
Ligands: NVP, MG
Released: 3 Apr 1996

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

Secondary structure: helices and β-sheets

1VRT contains 49 α-helices and 58 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: 26 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	12	1	1
α-helix	13	1
β-strand	20	1	2
α-helix	22-25	4
α-helix	28-43	16
β-strand	47-49	3	3
β-strand	57	1	2
β-strand	58	1	3
β-strand	60-64	5	4
β-strand	71-75	5	4
α-helix	78-83	6
β-strand	84	1	1
α-helix	85-86	2
α-helix	97-99	3
β-strand	105-110	6	5
α-helix	111	1
β-strand	112	1	6
α-helix	115-117	3
β-strand	119	1	7
α-helix	125-128	4
β-strand	130-131	2	3
β-strand	143-146	4	3
β-strand	148	1	7
α-helix	149-150	2
α-helix	156-174	19
β-strand	179-183	5	5
β-strand	186-191	6	5
α-helix	195-210	16
β-strand	215	1	6
α-helix	219-221	3
β-strand	227-229	3	8
β-strand	232-234	3	8
β-strand	239-241	3	8
β-strand	252-253	2	9
α-helix	254-267	14
α-helix	277-281	5
β-strand	292-293	2	9
α-helix	294-296	3
α-helix	297-311	15
β-strand	316	1	8
α-helix	317-319	3
β-strand	326-333	8	10
β-strand	336-344	9	10
β-strand	347-354	8	10
β-strand	361-362	2	11
α-helix	364-383	20
β-strand	388-391	4	10
α-helix	395-404	10
β-strand	414-416	3	10
α-helix	422-423	2
α-helix	433-434	2
β-strand	439-442	4	12
β-strand	456-459	4	12
β-strand	464-466	3	12
α-helix	474-488	15
β-strand	492-497	6	12
α-helix	500-507	8
β-strand	512-513	2	11
α-helix	516-527	12
β-strand	530-535	6	12

Chain B: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	13
β-strand	20	1	14
α-helix	21-25	5
α-helix	28-43	16
β-strand	47-49	3	15
β-strand	57	1	14
β-strand	58	1	15
β-strand	60-64	5	16
α-helix	65	1
β-strand	71-75	5	16
α-helix	78-83	6
β-strand	84	1	13
α-helix	85-86	2
α-helix	100-102	3
β-strand	105-110	6	17
α-helix	112-117	6
β-strand	119	1	18
α-helix	125-128	4
β-strand	130-132	3	15
α-helix	135-137	3
β-strand	142-146	5	15
β-strand	148	1	18
α-helix	149-150	2
α-helix	155-159	5
α-helix	161-174	14
β-strand	179-183	5	17
β-strand	186-191	6	17
α-helix	195-210	16
β-strand	232-234	3	17
α-helix	236-238	3
β-strand	253	1	19
α-helix	254-268	15
α-helix	277-281	5
β-strand	292	1	19
α-helix	297-309	13
α-helix	313-314	2
β-strand	326-331	6	20
β-strand	336-344	9	20
β-strand	347-355	9	20
α-helix	364-383	20
α-helix	386-387	2
β-strand	388-391	4	20
α-helix	395-405	11
β-strand	413-416	4	20
α-helix	421-425	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 reverse transcriptase	A	protein	560	Human immunodeficiency virus 1	P04585 (AlphaFold model)
HIV-1 reverse transcriptase	B	protein	440	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1VRT_1 HIV-1 REVERSE TRANSCRIPTASE (chains A)
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPV
FAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL
DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVI
YQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT
VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA
HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTP
PLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQ
AIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHK
GIGGNEQVDKLVSAGIRKVL

Sequence of entity 2 (B), FASTA

>1VRT_2 HIV-1 REVERSE TRANSCRIPTASE (chains B)
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPV
FAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL
DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVI
YQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT
VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA
HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTP
PLVKLWYQLEKEPIVGAETF

Ligands and cofactors

ID	Name	Formula	Copies
NVP	11-cyclopropyl-5,11-dihydro-4-methyl-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-…	C15 H14 N4 O	1
MG	Magnesium ion	Mg	1

Primary citation

High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Ren, J., Esnouf, R., Garman, E. et al. Nat Struct Biol (1995) 2:293-302. DOI 10.1038/nsb0495-293 · PubMed

Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DV4 1.14 Å, HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with…
6DIF 1.2 Å, Wild-type HIV-1 protease in complex with tipranavir
6DV0 1.2 Å, HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine…
5DGU 1.22 Å, Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted…
6E9A 1.22 Å, HIV-1 wild type protease with grl-034-17A, (3aS, 5R, 6aR)-2-oxohexahyd…
6DJ1 1.26 Å, Wild-type HIV-1 protease in complex with Lopinavir
8F0F 1.29 Å, HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on…
6E7J 1.3 Å, HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one…
6DJ7 1.31 Å, HIV-1 protease with mutation L76V in complex with GRL-5010…
8ESX 1.35 Å, HIV protease in complex with benzoxaborolone analog of darunavir
8ESY 1.35 Å, D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir

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Drugs bound to their targets

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