MolNFT v1 · #137135 · protein + DNA
DNA polymerase beta substrate complex with 8-OXOG:A at the primer terminus and incoming dctp analog
5VEZ · DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “DNA polymerase beta substrate complex with 8-OXOG:A at the primer terminus and incoming dctp analog”. X-ray diffraction, 3 ligands (XC5, NA, MG), 3 pockets (best…
- PDB
- 5VEZ
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- XC5, NA, MG
- Pockets
- 3 · best druggability 0.71
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*GP*AP*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*(8OG))-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 | 326 | 51% helix, 13% strand | P06746 |
Ligands and binding sites
- XC5 · 2'-deoxy-5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains T, P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, D
- MG · Magnesium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.71 | 0.76 | 60 | NA, MG, XC5 |
| 2 | 349 | 0.62 | 0.79 | 29 | empty |
| 3 | 206 | 0.58 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–A · 738 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 462 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- P–A · 383 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 369 Ų buried · 7 hydrogen bonds · protein-nucleic
- T–D · 227 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5VEZ · DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming… · the same entry in another collection · chain T against T, 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 5VEZ · PDBe 5VEZ · UniProt P06746
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