Research workbench
Structure of a catalytic complex of HIV-1 reverse transcriptase: implications for nucleoside analog drug resistance
Analyse Structure of a catalytic complex of HIV-1 reverse transcriptase: implications… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RTD
- Type
- protein + DNA
- Length
- 2,028 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA template for reverse transcriptase; DNA primer for reverse transcriptase; Protein…
- EC
- 2.7.7.49
- UniProt
- P03366, P04585
- Ligands
- TTP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | DNA template for reverse transcriptase | dna | 25 | — | — |
| F, H | DNA primer for reverse transcriptase | dna | 21 | — | — |
| A, C | Protein (reverse transcriptase) (EC 2.7.7.49) | protein | 554 | 31% helix, 23% strand | P03366 |
| B, D | Protein (reverse transcriptase) (EC 2.7.7.49) | protein | 414 | 35% helix, 18% strand | P04585 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains E, F, A, G, H, C
- MG · Magnesium ion · metal · 6 copies · chains A, F, E, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.86 | 0.87 | 102 | empty |
| 2 | 1183 | 0.85 | 0.86 | 104 | empty |
| 3 | 842 | 0.84 | 0.86 | 99 | empty |
| 4 | 1063 | 0.82 | 0.83 | 101 | empty |
| 5 | 799 | 0.74 | 0.78 | 72 | empty |
Interfaces
13 interfaces between chains.
- C–D · 3032 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3012 Ų buried · 37 hydrogen bonds · protein-protein
- E–A · 1449 Ų buried · 14 hydrogen bonds · protein-nucleic
- G–C · 1413 Ų buried · 14 hydrogen bonds · protein-nucleic
- H–C · 971 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1RTD · Structure of a catalytic complex of HIV-1 reverse transcriptase: implications for… · the same entry in another collection · chain E against E, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03366
- Every structure of UniProt P04585
- Elsewhere: RCSB PDB 1RTD · PDBe 1RTD · UniProt P03366 · UniProt P04585
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