Research workbench
NGTET1 in complex with 5MC DNA in space group P3221
Analyse NGTET1 in complex with 5MC DNA in space group P3221 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CG9
- Type
- protein + DNA
- Length
- 578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tet-like dioxygenase; DNA (5'-D(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'); DNA…
- UniProt
- D2W6T1
- Ligands
- AKG, MN, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tet-like dioxygenase | protein | 267 | 34% helix, 25% strand | D2W6T1 |
| B, E | DNA (5'-D(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*TP*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3') | dna | 12 | — | — |
| D | Tet-like dioxygenase | protein | 264 | 33% helix, 27% strand | D2W6T1 |
| F | DNA (5'-D(*TP*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C, D, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.75 | 0.99 | 21 | AKG, MN |
| 2 | 62 | 0.72 | 0.98 | 21 | AKG, MN |
| 3 | 298 | 0.65 | 0.82 | 30 | empty |
| 4 | 397 | 0.64 | 0.79 | 38 | empty |
| 5 | 169 | 0.55 | 0.80 | 37 | SO4, EDO |
Interfaces
7 interfaces between chains.
- A–D · 982 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 555 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–F · 553 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–F · 530 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–C · 499 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 D2W6T1
- Elsewhere: RCSB PDB 5CG9 · PDBe 5CG9 · UniProt D2W6T1
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