Research workbench
Human DNA polymerase eta - DNA ternary complex with the 5'T of a cpd in the active site (TT2)
Analyse Human DNA polymerase eta - DNA ternary complex with the 5'T of a cpd in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SI8
- Type
- protein + DNA
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*TP*A*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DZ4, 3D1, MG, CO
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 422 | 45% helix, 20% strand | Q9Y253 |
| T | DNA (5'-D(*TP*A*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*C)-3') | dna | 10 | — | — |
| P | DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, T, P
- 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, P
- CO · Cobalt (II) ion · metal · chains A
- GOL · Glycerol · additive · 8 copies · chains A, P
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, P
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.84 | 0.86 | 76 | DZ4, 3D1, MG |
| 2 | 429 | 0.72 | 0.83 | 37 | empty |
| 3 | 166 | 0.47 | 0.77 | 17 | empty |
| 4 | 76 | 0.43 | 0.80 | 14 | empty |
| 5 | 108 | 0.39 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 913 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 656 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 402 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SI8 · Human DNA polymerase eta - DNA ternary complex with the 5'T of a CPD in the active site… · 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 3SI8 · PDBe 3SI8 · UniProt Q9Y253
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