Research workbench
Structure of hpoleta incorporating dctp opposite the 3-prime PT(DACH)- gg
Analyse Structure of hpoleta incorporating dctp opposite the 3-prime PT(DACH)- gg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MXO
- Type
- protein + DNA
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*AP*CP*GP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 0KX, 9RD, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 428 | 45% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*AP*CP*GP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 10 | — | — |
| P | DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, T, P
- 9RD · (cyclohex-1-ene-1,2-diamine)platinum(2+) · ligand · chains T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.78 | 0.80 | 69 | 0KX, MG |
| 2 | 561 | 0.74 | 0.82 | 48 | 9RD |
| 3 | 246 | 0.66 | 0.83 | 26 | empty |
| 4 | 106 | 0.41 | 0.77 | 18 | empty |
| 5 | 83 | 0.38 | 0.77 | 15 | GOL |
Interfaces
3 interfaces between chains.
- A–T · 867 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–P · 612 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 384 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 6MXO · Structure of HPoleta incorporating dCTP opposite the 3-prime Pt(DACH)-GG · 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 Q9Y253
- Elsewhere: RCSB PDB 6MXO · PDBe 6MXO · UniProt Q9Y253
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