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
- 6H1V
- Type
- protein + DNA
- Length
- 1,140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon catalytic subunit a; DNA…
- EC
- 2.7.7.7
- UniProt
- P21951
- Ligands
- SF4, DTP, MG
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 1114 | 41% helix, 22% strand | P21951 |
| P | DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3') | dna | 11 | — | — |
| T | DNA (5'-D(P*AP*AP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.75 | 0.78 | 83 | DTP |
| 2 | 855 | 0.70 | 0.76 | 80 | empty |
| 3 | 743 | 0.69 | 0.76 | 62 | empty |
| 4 | 294 | 0.69 | 0.84 | 48 | empty |
| 5 | 194 | 0.64 | 0.84 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1193 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 728 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 489 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6H1V · 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 0.99
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 6H1V · PDBe 6H1V · UniProt P21951
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.