1RTD
STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
F [auth B] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8036908 | 3001272 | SCOP2B (2022-06-29) |
F [auth B] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8036908 | 3001272 | SCOP2B (2022-06-29) |
H [auth D] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8036908 | 3001272 | SCOP2B (2022-06-29) |
H [auth D] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8036908 | 3001272 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Ribonuclease H-like | 8075088 | 3000143 | SCOP2B (2022-06-29) |
G [auth C] | SCOP2B Superfamily | Ribonuclease H-like | 8075088 | 3000143 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
F [auth B] | RVT_thumb | e1rtdB3 | A: alpha bundles | X: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | H: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | T: helical bundle domain in reverse transcriptase-like polymerases | F: RVT_thumb | ECOD (1.6) |
F [auth B] | RVT_1 | e1rtdB2 | A: a+b two layers | X: Alpha-beta plaits | H: Adenylyl and guanylyl cyclase catalytic domain-like | T: Adenylyl and guanylyl cyclase catalytic domain-like | F: RVT_1 | ECOD (1.6) |
F [auth B] | RVT_connect | e1rtdB1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: RNaseH-like domain in reverse transcriptase (From Topology) | T: RNaseH-like domain in reverse transcriptase | F: RVT_connect | ECOD (1.6) |
H [auth D] | RVT_thumb | e1rtdD1 | A: alpha bundles | X: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | H: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | T: helical bundle domain in reverse transcriptase-like polymerases | F: RVT_thumb | ECOD (1.6) |
H [auth D] | RVT_1 | e1rtdD2 | A: a+b two layers | X: Alpha-beta plaits | H: Adenylyl and guanylyl cyclase catalytic domain-like | T: Adenylyl and guanylyl cyclase catalytic domain-like | F: RVT_1 | ECOD (1.6) |
H [auth D] | RVT_connect | e1rtdD3 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: RNaseH-like domain in reverse transcriptase (From Topology) | T: RNaseH-like domain in reverse transcriptase | F: RVT_connect | ECOD (1.6) |
E [auth A] | RVT_thumb | e1rtdA7 | A: alpha bundles | X: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | H: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | T: helical bundle domain in reverse transcriptase-like polymerases | F: RVT_thumb | ECOD (1.6) |
E [auth A] | RVT_1 | e1rtdA8 | A: a+b two layers | X: Alpha-beta plaits | H: Adenylyl and guanylyl cyclase catalytic domain-like | T: Adenylyl and guanylyl cyclase catalytic domain-like | F: RVT_1 | ECOD (1.6) |
E [auth A] | RNase_H | e1rtdA6 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: RNase_H | ECOD (1.6) |
E [auth A] | RVT_connect | e1rtdA5 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: RNaseH-like domain in reverse transcriptase (From Topology) | T: RNaseH-like domain in reverse transcriptase | F: RVT_connect | ECOD (1.6) |
G [auth C] | RVT_thumb | e1rtdC7 | A: alpha bundles | X: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | H: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | T: helical bundle domain in reverse transcriptase-like polymerases | F: RVT_thumb | ECOD (1.6) |
G [auth C] | RVT_1 | e1rtdC8 | A: a+b two layers | X: Alpha-beta plaits | H: Adenylyl and guanylyl cyclase catalytic domain-like | T: Adenylyl and guanylyl cyclase catalytic domain-like | F: RVT_1 | ECOD (1.6) |
G [auth C] | RNase_H | e1rtdC6 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: RNase_H | ECOD (1.6) |
G [auth C] | RVT_connect | e1rtdC5 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: RNaseH-like domain in reverse transcriptase (From Topology) | T: RNaseH-like domain in reverse transcriptase | F: RVT_connect | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
F [auth B], H [auth D] | PF06817 | Reverse transcriptase thumb domain (RVT_thumb) | Reverse transcriptase thumb domain | This domain is known as the thumb domain. It is composed of a four helix bundle [1]. | Domain |
F [auth B], H [auth D] | PF06815 | Reverse transcriptase connection domain (RVT_connect) | Reverse transcriptase connection domain | This domain is known as the connection domain. This domain lies between the thumb and palm domains [1]. | Domain |
F [auth B], H [auth D] | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1) | Reverse transcriptase (RNA-dependent DNA polymerase) | A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ... | Domain |
E [auth A], G [auth C] | PF06817 | Reverse transcriptase thumb domain (RVT_thumb) | Reverse transcriptase thumb domain | This domain is known as the thumb domain. It is composed of a four helix bundle [1]. | Domain |
E [auth A], G [auth C] | PF06815 | Reverse transcriptase connection domain (RVT_connect) | Reverse transcriptase connection domain | This domain is known as the connection domain. This domain lies between the thumb and palm domains [1]. | Domain |
E [auth A], G [auth C] | PF00075 | RNase H (RNase_H) | RNase H | RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. | Domain |
E [auth A], G [auth C] | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1) | Reverse transcriptase (RNA-dependent DNA polymerase) | A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
HIV-1 reverse transcriptase M-CSA #1000 | HIV-1 reverse transcriptase (RT) is a component of gag-pol polyprotein encoded by the human immunodeficiency virus-1 (HIV-1) genome. HIV-1 reverse transcriptase contains both DNA polymerase and ribonuclease H (RNase H) activities to convert the viral genomic RNA to double-stranded DNA, which is then integrated into the host genome and replicated along with the infected host cells. Understanding the HIV-1 reverse transcriptase catalytic mechanism is key for discovery of potent drugs and development of more effective, less toxic drugs and multi-drug combinations. | Defined by 5 residues: ASP:E-110 [auth A-110]VAL:E-111 [auth A-111]ASP:E-185 [auth A-185]ASP:E-186 [auth A-186]LYS:E-220 [auth A-220] | EC: 2.7.7.49 (PDB Primary Data) |