MolNFT v1 · #137545 · protein + DNA
Human DNA polymerase beta pre-catalytic 8-OXOG:DC extension complex with dttp bound in non-planar conformation
5VRW · DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)…: “Human DNA polymerase beta pre-catalytic 8-OXOG:DC extension complex with dttp bound in non-planar conformation”. X-ray diffraction, 2 ligands (TTP, CA), 3 pockets (best druggability 0.75).…
- PDB
- 5VRW
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- TTP, CA
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3') | dna | 16 | — | — |
| P | DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 51% helix, 13% strand | P06746 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains T, P, A
- CA · Calcium ion · metal · 7 copies · chains P, A, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.75 | 0.79 | 70 | TTP, CA |
| 2 | 214 | 0.56 | 0.79 | 24 | empty |
| 3 | 77 | 0.39 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- T–A · 682 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 460 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- P–A · 391 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 381 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–D · 207 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5VRW · Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in… · the same entry in another collection · chain P against P, 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 0.93
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 5VRW · PDBe 5VRW · UniProt P06746
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