MolNFT v1 · #146463 · protein + DNA
DNA polymerase beta substrate complex with templating cytosine and incoming fapy-dgtp analog
6DIA: “DNA polymerase beta substrate complex with templating cytosine and incoming fapy-dgtp analog”. X-ray diffraction, 3 ligands (GKS, CA, NA), 2 pockets (best druggability 0.71). MolNFT v1 #146463 on GenesisL1: 3D structure, binding…
- PDB
- 6DIA
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- GKS, CA, NA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 52% helix, 13% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- GKS · 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol · ligand · chains A, T, P
- CA · Calcium ion · metal · 3 copies · chains A, T
- NA · Sodium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.71 | 0.75 | 83 | GKS, CA, NA |
| 2 | 210 | 0.60 | 0.82 | 27 | empty |
Interfaces
5 interfaces between chains.
- T–P · 466 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–T · 382 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 370 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 305 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–D · 231 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DIA · DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP… · the same entry in another collection · chain D against D, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P06746
- Elsewhere: RCSB PDB 6DIA · PDBe 6DIA · UniProt P06746
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