MolNFT v1 · #137549 · protein + DNA
Human DNA polymerase beta 8-OXOG:DC extension with dttp after 80 S
5VS0: “Human DNA polymerase beta 8-OXOG:DC extension with dttp after 80 S”. X-ray diffraction, 3 ligands (PPV, MG, CL), 4 pockets (best druggability 0.70). MolNFT v1 #137549 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VS0
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- PPV, MG, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 51% helix, 14% strand | P06746 |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*CP*T)-3') | dna | 11 | — | — |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3') | dna | 16 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A, P
- MG · Magnesium ion · metal · 6 copies · chains A, P, D, T
- CL · Chloride ion · ion · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.70 | 0.76 | 53 | MG, PPV |
| 2 | 413 | 0.65 | 0.79 | 33 | empty |
| 3 | 225 | 0.58 | 0.80 | 24 | empty |
| 4 | 51 | 0.28 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–T · 742 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 549 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 492 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–D · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–T · 229 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 5VS0 · PDBe 5VS0 · UniProt P06746
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