MolNFT v1 · #103460 · protein + DNA
Structure of human DNA polymerase beta complexed with a in the template base paired with incoming non-hydrolyzable CTP and manganese
4PHD: “Structure of human DNA polymerase beta complexed with a in the template base paired with incoming…”. X-ray diffraction, 3 ligands (0KX, MN, NA), 3 pockets (best druggability 0.74). MolNFT v1 #103460 on GenesisL1: 3D structure…
- PDB
- 4PHD
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 0KX, MN, NA
- Pockets
- 3 · best druggability 0.74
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 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*AP*TP*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*A)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, 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 | 895 | 0.74 | 0.78 | 70 | MN, 0KX |
| 2 | 232 | 0.60 | 0.81 | 27 | empty |
| 3 | 81 | 0.57 | 0.87 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–T · 594 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 474 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–P · 386 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 372 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–D · 232 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 4PHD · Structure of human DNA polymerase beta complexed with A in the template base paired with… · the same entry in another collection · chain A against A, 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 4PHD · PDBe 4PHD · UniProt P06746
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