MolNFT v1 · #9380 · protein + DNA
Crystal structure of DNA polymerase beta complexed with DNA and cr-tmppcp
1HUO · 5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3': “Crystal structure of DNA polymerase beta complexed with DNA and cr-tmppcp”. X-ray diffraction, 2 ligands (TTE, CR), 8 pockets (best druggability 0.60). MolNFT v1 #9380 on GenesisL1: 3D…
- PDB
- 1HUO
- Type
- protein + DNA
- Length
- 680 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3'; 5'-D(P*CP*GP*AP*CP*GP*CP*C)-3'; DNA polymerase…
- EC
- 2.7.7.7
- UniProt
- P06766
- Ligands
- TTE, CR
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, C | 5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3' | dna | 8 | — | — |
| P, D | 5'-D(P*CP*GP*AP*CP*GP*CP*C)-3' | dna | 7 | — | — |
| A, B | DNA polymerase beta (EC 2.7.7.7) | protein | 325 | 47% helix, 13% strand | P06766 |
Ligands and binding sites
- TTE · Phosphomethyl phosphonic acid deoxythymidylate ester · ligand · 2 copies · chains T, P, A, C, D, B
- CR · Chromium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.60 | 0.76 | 46 | CR, TTE |
| 2 | 233 | 0.60 | 0.81 | 24 | empty |
| 3 | 224 | 0.58 | 0.80 | 24 | empty |
| 4 | 331 | 0.58 | 0.77 | 34 | CR, TTE |
| 5 | 121 | 0.36 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–B · 642 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–A · 620 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–A · 370 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–B · 366 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 341 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 1HUO · Crystal structure of DNA polymerase beta complexed with DNA and cr-tmppcp · the same entry in another collection · chain B against B, TM-score 1.00
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P06766
- Elsewhere: RCSB PDB 1HUO · PDBe 1HUO · UniProt P06766
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