MolNFT v1 · #67704 · protein + DNA
Ternary complex of human DNA polymerase beta with an abasic site (thf): dapcpp mismatch
3ISD: “Ternary complex of human DNA polymerase beta with an abasic site (thf): dapcpp mismatch”. X-ray diffraction, 3 ligands (F2A, MN, NA), 3 pockets (best druggability 0.76). MolNFT v1 #67704 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ISD
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5'-D(P*GP*TP*CP*GP*G)-3'; 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- F2A, MN, NA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 50% helix, 12% strand | P06746 |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3' | dna | 10 | — | — |
| T | 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3' | dna | 16 | — | — |
Ligands and binding sites
- F2A · 2'-deoxy-5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]adenosine · ligand · chains A, P, T
- MN · Manganese (II) ion · metal · 8 copies · chains A, P, D, T
- NA · Sodium ion · metal · 3 copies · chains A, P, D
- EDO · 1,2-ethanediol · additive · 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 | 1110 | 0.76 | 0.79 | 83 | MN, F2A |
| 2 | 294 | 0.64 | 0.81 | 27 | empty |
| 3 | 329 | 0.59 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–T · 550 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 468 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–D · 393 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 348 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–T · 241 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3ISD · Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch · the same entry in another collection · chain D against D, 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 0.96
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 3ISD · PDBe 3ISD · UniProt P06746
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