MolNFT v1 · #79680 · protein + DNA
5-hydroxycytosine paired with damp in RB69 GP43
3TAE · DNA (5'-D(*CP*CP*(5OC) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP…: “5-hydroxycytosine paired with damp in RB69 GP43”. X-ray diffraction, 2 ligands (5OC, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #79680 on GenesisL1: 3D…
- PDB
- 3TAE
- Type
- protein + DNA
- Length
- 3,721 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*(5OC) P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- 5OC, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'-D(*CP*CP*(5OC) 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*(5OC) 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*(5OC) 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*(5OC) 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 | — | — |
| A, C | DNA polymerase (EC 2.7.7.7) | protein | 903 | 43% helix, 18% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 901 | 42% helix, 19% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 898 | 40% helix, 18% strand | Q38087 |
Ligands and binding sites
- 5OC · 2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains G, B, K, D
- SO4 · Sulfate ion · ion · 4 copies · chains F, H, B, C
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 | 304 | 0.84 | 0.95 | 33 | empty |
| 2 | 361 | 0.82 | 0.92 | 36 | empty |
| 3 | 1114 | 0.82 | 0.83 | 98 | empty |
| 4 | 267 | 0.81 | 0.93 | 30 | empty |
| 5 | 810 | 0.79 | 0.82 | 82 | empty |
Interfaces
16 interfaces between chains.
- I–C · 1061 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–A · 1009 Ų buried · 11 hydrogen bonds · protein-nucleic
- G–B · 815 Ų buried · 10 hydrogen bonds · protein-nucleic
- J–C · 812 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 733 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 3TAE · 5-hydroxycytosine paired with dAMP in RB69 gp43 · 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 Q38087
- Elsewhere: RCSB PDB 3TAE · PDBe 3TAE · UniProt Q38087
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