MolNFT v1 · #99646 · protein + DNA
DNA polymerase beta E295K soaked with datp
4M9N: “DNA polymerase beta E295K soaked with datp”. X-ray diffraction, 3 ligands (DTP, NA, MG), 2 pockets (best druggability 0.74). MolNFT v1 #99646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4M9N
- Type
- protein + DNA
- Length
- 331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA template strand; DNA primer strand; DNA downstream strand
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DTP, NA, MG
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 300 | 53% helix, 13% strand | P06746 |
| T | DNA template strand | dna | 16 | — | — |
| P | DNA primer strand | dna | 10 | — | — |
| D | DNA downstream strand | dna | 5 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- MG · Magnesium ion · metal · chains A
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 | 1038 | 0.74 | 0.77 | 82 | MG, DTP |
| 2 | 243 | 0.62 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–P · 474 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–T · 429 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 339 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–P · 322 Ų buried · 7 hydrogen bonds · protein-nucleic
- T–D · 231 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
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 4M9N · PDBe 4M9N · UniProt P06746
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