Research workbench
The crystal structure of POL2CORE in complex with DNA and an incoming nucleotide, carrying an fe-S cluster
Analyse The crystal structure of POL2CORE in complex with DNA and an incoming… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QIB
- Type
- protein + DNA
- Length
- 1,149 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon catalytic subunit a; PRIMER_11DDC; TEMPLATE16
- EC
- 2.7.7.7
- UniProt
- P21951
- Ligands
- SF4, DTP, CA
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 1123 | 40% helix, 22% strand | P21951 |
| P | PRIMER_11DDC | dna | 11 | — | — |
| T | TEMPLATE16 | dna | 15 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.77 | 0.80 | 62 | DTP, CA |
| 2 | 643 | 0.71 | 0.79 | 58 | empty |
| 3 | 619 | 0.70 | 0.78 | 63 | empty |
| 4 | 326 | 0.68 | 0.83 | 40 | empty |
| 5 | 142 | 0.59 | 0.84 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1326 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–P · 796 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–T · 501 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6QIB · The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide… · the same entry in another collection · chain A against A, TM-score 1.00
- P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P21951
- Elsewhere: RCSB PDB 6QIB · PDBe 6QIB · UniProt P21951
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