MolNFT v1 · #122878 · protein + DNA
HIV-1 reverse transcriptase in complex with DNA that has incorporated efda-mp at the P-(post-translocation) site and dtmp at the N-(pre- translocation) site
5J2N · Reverse transcriptase, P66 domain: “HIV-1 reverse transcriptase in complex with DNA that has incorporated efda-mp at the P-(post-translocation)…”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5J2N
- Type
- protein + DNA
- Length
- 1,005 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase, P66 domain; Reverse transcriptase, P51 domain; DNA 5'…
- EC
- 2.7.7.-
- UniProt
- P04585
- Ligands
- MG
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase, P66 domain (EC 2.7.7.-) | protein | 558 | 32% helix, 24% strand | P04585 |
| B | Reverse transcriptase, P51 domain (EC 2.7.7.-) | protein | 405 | 37% helix, 21% strand | P04585 |
| P | DNA 5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3' | dna | 19 | — | — |
| T | DNA (27-mer) | dna | 23 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.86 | 0.89 | 74 | empty |
| 2 | 979 | 0.85 | 0.87 | 87 | empty |
| 3 | 482 | 0.71 | 0.81 | 43 | empty |
| 4 | 546 | 0.71 | 0.80 | 47 | empty |
| 5 | 64 | 0.67 | 0.95 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3048 Ų buried · 30 hydrogen bonds · protein-protein
- A–T · 1372 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 1256 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 894 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- B–P · 116 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5J2N · HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the… · the same entry in another collection · chain T against T, 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 P04585
- Elsewhere: RCSB PDB 5J2N · PDBe 5J2N · UniProt P04585
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