MolNFT v1 · #102037 · protein + DNA
Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA
4O9M · DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA”. X-ray diffraction, 2 ligands (2RW, NA), 3 pockets (best druggability…
- PDB
- 4O9M
- Type
- protein + DNA
- Length
- 358 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*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 2RW, NA
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
| C | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') | dna | 11 | — | — |
| D | (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 | 52% helix, 13% strand | P06746 |
Ligands and binding sites
- 2RW · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains D, A
- NA · Sodium ion · metal · 2 copies · chains C, A, D
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 | 854 | 0.68 | 0.75 | 66 | empty |
| 2 | 252 | 0.64 | 0.82 | 29 | empty |
| 3 | 229 | 0.64 | 0.83 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–A · 520 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 519 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- B–A · 438 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 351 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 227 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4O9M · Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site)… · the same entry in another collection · chain B against B, 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 0.94
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 4O9M · PDBe 4O9M · UniProt P06746
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