Research workbench
5-fluorocytosine paired with damp in RB69 GP43
Analyse 5-fluorocytosine paired with damp in RB69 GP43 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TAG
- Type
- protein + DNA
- Length
- 3,724 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*CP*CP*(C37) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- C37, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 12 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 906 | 43% helix, 18% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 901 | 41% helix, 19% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 19% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 898 | 39% helix, 18% strand | Q38087 |
| E | DNA (5'-D(*CP*CP*(C37) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| F | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*A)- 3') | dna | 14 | — | — |
| I | DNA (5'-D(*CP*CP*(C37) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 17 | — | — |
| J | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*A)- 3') | dna | 15 | — | — |
| G | DNA (5'-D(*CP*CP*(C37) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 15 | — | — |
| H | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*A)- 3') | dna | 13 | — | — |
| K | DNA (5'-D(*CP*CP*(C37) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 13 | — | — |
| L | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*A)- 3') | dna | 11 | — | — |
Ligands and binding sites
- C37 · 5-fluoro-2'-deoxy-cytidine-5'-monophosphate · ligand · 2 copies · chains B, G, D, K
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.84 | 0.95 | 32 | empty |
| 2 | 267 | 0.82 | 0.93 | 30 | empty |
| 3 | 715 | 0.81 | 0.85 | 69 | empty |
| 4 | 356 | 0.81 | 0.91 | 39 | empty |
| 5 | 836 | 0.79 | 0.82 | 76 | empty |
Interfaces
16 interfaces between chains.
- C–I · 1088 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–E · 1042 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–G · 810 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–J · 794 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 769 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 3TAG · 5-fluorocytosine paired with dAMP in RB69 gp43 · the same entry in another collection · chain H against H, 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 Q38087
- Elsewhere: RCSB PDB 3TAG · PDBe 3TAG · UniProt Q38087
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