MolNFT v1 · #99457 · protein + DNA
RB69 DNA polymerase ternary complex with DG/DT at position N-4 of PRIMER/TEMPLATE duplex
4M42: “RB69 DNA polymerase ternary complex with DG/DT at position N-4 of PRIMER/TEMPLATE duplex”. X-ray diffraction, 2 ligands (ATP, CA), 11 pockets (best druggability 0.82). MolNFT v1 #99457 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4M42
- Type
- protein + DNA
- Length
- 933 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA template; DNA primer
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- ATP, CA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 45% helix, 19% strand | Q38087 |
| T | DNA template | dna | 17 | — | — |
| P | DNA primer | dna | 13 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 5 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.82 | 0.91 | 36 | empty |
| 2 | 989 | 0.80 | 0.81 | 73 | CA |
| 3 | 1187 | 0.77 | 0.79 | 107 | ATP, CA |
| 4 | 374 | 0.59 | 0.76 | 28 | empty |
| 5 | 130 | 0.57 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1087 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 588 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–P · 580 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4M42 · RB69 DNA polymerase ternary complex with dG/dT at position n-4 of primer/tempLate duplex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38087
- Elsewhere: RCSB PDB 4M42 · PDBe 4M42 · UniProt Q38087
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