MolNFT v1 · #101252 · protein + DNA
Structure of human DNA polymerase beta complexed with 8BRG in the template base-paired with incoming non-hydrolyzable CTP
4NLK · 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “Structure of human DNA polymerase beta complexed with 8BRG in the template base-paired with incoming…”. X-ray diffraction, 3 ligands (0KX, MG, NA), 3 pockets (best…
- PDB
- 4NLK
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 0KX, MG, NA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3' | dna | 10 | — | — |
| 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 | 50% helix, 13% strand | P06746 |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains T, P, A
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains P, 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 | 965 | 0.72 | 0.76 | 62 | MG, 0KX |
| 2 | 310 | 0.60 | 0.78 | 27 | empty |
| 3 | 233 | 0.57 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- T–A · 742 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 477 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- P–A · 389 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 383 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 239 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4NLK · Structure of human DNA polymerase beta complexed with 8BrG in the template base-paired… · 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 0.94
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 4NLK · PDBe 4NLK · UniProt P06746
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