Research workbench
DNA polymerase beta mismatched product complex with MN2+, 30 min
Analyse DNA polymerase beta mismatched product complex with MN2+, 30 min in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KLT
- Type
- protein + DNA
- Length
- 346 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*CP*A)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- PPV, MN, NA, CL
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 314 | 52% 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*CP*A)-3' | dna | 11 | — | — |
| T | 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A, P
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- 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 | 976 | 0.76 | 0.79 | 82 | MN, PPV |
| 2 | 276 | 0.64 | 0.82 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–P · 554 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 495 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–T · 425 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 384 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–T · 237 Ų buried · 27 hydrogen bonds · nucleic-nucleic
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 4KLT · PDBe 4KLT · UniProt P06746
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