Research workbench
Human DNA polymerase eta - DNA ternary complex with a cpd 2BP upstream of the active site (TT4)
Analyse Human DNA polymerase eta - DNA ternary complex with a cpd 2BP upstream of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MR6
- Type
- protein + DNA
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*C*AP*TP*CP*AP*(TTD)P*AP*CP*GP*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 427 | 44% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*C*AP*TP*CP*AP*(TTD)P*AP*CP*GP*AP*GP*C)-3') | dna | 10 | — | — |
| P | DNA (5'-D(*TP*CP*TP*CP*GP*TP*AP*AP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 2 copies · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · 7 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 | 1043 | 0.79 | 0.81 | 67 | XG4, MG, GOL |
| 2 | 463 | 0.71 | 0.81 | 42 | empty |
| 3 | 232 | 0.68 | 0.85 | 26 | GOL |
| 4 | 74 | 0.39 | 0.78 | 20 | empty |
| 5 | 91 | 0.39 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 982 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 703 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 372 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3MR6 · Human DNA polymerase eta - DNA ternary complex with a CPD 2bp upstream of 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 3MR6 · PDBe 3MR6 · UniProt Q9Y253
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