MolNFT v1 · #106231 · protein + DNA
Ternary complex crystal structure of DNA polymerase beta with (alpha, beta)-CH2-(BETA,GAMMA)-nh-dttp
4RT2: “Ternary complex crystal structure of DNA polymerase beta with (alpha, beta)-CH2-(BETA,GAMMA)-nh-dttp”. X-ray diffraction, 4 ligands (N6T, NA, MG), 2 pockets (best druggability 0.76). MolNFT v1 #106231 on GenesisL1: 3D structure…
- PDB
- 4RT2
- 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*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- N6T, NA, MG, CL
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 13% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*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*(DOC))-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- N6T · 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine · ligand · chains A, T, P
- NA · Sodium ion · metal · 3 copies · chains A, P, D
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.76 | 0.79 | 74 | N6T |
| 2 | 222 | 0.58 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–T · 728 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 471 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–D · 383 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 366 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 235 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 4RT2 · PDBe 4RT2 · UniProt P06746
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