MolNFT v1 · #19127 · protein + DNA
Crystal structures of the N-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain
1QAI · DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3'): “Crystal structures of the N-terminal fragment from moloney murine leukemia virus reverse transcriptase…”. X-ray diffraction, 1 ligand (HG), 5 pockets (best druggability 0.60). MolNFT v1…
- PDB
- 1QAI
- Type
- protein + DNA
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3'); Reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P03355
- Ligands
- HG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3') | dna | 8 | — | — |
| A, B | Reverse transcriptase (EC 2.7.7.49) | protein | 251 | 32% helix, 24% strand | P03355 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.60 | 0.77 | 41 | empty |
| 2 | 227 | 0.54 | 0.77 | 27 | empty |
| 3 | 121 | 0.45 | 0.78 | 23 | empty |
| 4 | 99 | 0.43 | 0.78 | 21 | empty |
| 5 | 57 | 0.26 | 0.73 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 365 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- D–B · 292 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 210 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–A · 209 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–A · 197 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1QAI · Crystal structures of the N-terminal fragment from moloney murine leukemia virus reverse… · the same entry in another collection · chain A against A, 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 P03355
- Elsewhere: RCSB PDB 1QAI · PDBe 1QAI · UniProt P03355
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