MolNFT v1 · #136211 · protein + DNA
Structure of human DNA polymerase iota bound to template 1-methyl- deoxyadenosine crystallized in the presence of dctp
5ULX · DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'): “Structure of human DNA polymerase iota bound to template 1-methyl- deoxyadenosine crystallized in the…”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5ULX
- Type
- protein + DNA
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'); DNA (5'-D(P*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3') | dna | 7 | — | — |
| T | DNA (5'-D(P*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3') | dna | 8 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 373 | 46% helix, 20% strand | Q9UNA4 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.77 | 0.79 | 85 | empty |
| 2 | 446 | 0.69 | 0.80 | 33 | empty |
| 3 | 68 | 0.28 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- T–A · 709 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–A · 474 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 330 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ULX · Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine… · the same entry in another collection · chain P against P, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · 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 Q9UNA4
- Elsewhere: RCSB PDB 5ULX · PDBe 5ULX · UniProt Q9UNA4
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