MolNFT v1 · #90172 · protein + DNA
Conformationally restrained north-methanocarba-2'-deoxyadenosine corrects the error-prone nature of human DNA polymerase iota
4EBD: “Conformationally restrained north-methanocarba-2'-deoxyadenosine corrects the error-prone nature of human DNA…”. X-ray diffraction, 2 ligands (0OJ, CA), 5 pockets (best druggability 0.75). MolNFT v1 #90172 on GenesisL1: 3D…
- PDB
- 4EBD
- Type
- protein + DNA
- Length
- 392 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- 0OJ, CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 376 | 44% helix, 19% strand | Q9UNA4 |
| P | 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 7 | — | — |
| T | 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3' | dna | 9 | — | — |
Ligands and binding sites
- 0OJ · South-methanocarba-2'-deoxyadenosine triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 3 copies · chains A, P
- GOL · Glycerol · additive · 2 copies · chains A, T, P
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 | 751 | 0.75 | 0.80 | 62 | empty |
| 2 | 471 | 0.70 | 0.81 | 36 | GOL |
| 3 | 395 | 0.65 | 0.79 | 36 | 0OJ, CA |
| 4 | 81 | 0.34 | 0.75 | 16 | empty |
| 5 | 61 | 0.29 | 0.75 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–T · 884 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 541 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 326 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4EBD · Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone… · the same entry in another collection · chain A against A, 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 4EBD · PDBe 4EBD · UniProt Q9UNA4
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