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DNA polymerase beta G231D crystallized in peg 400
Analyse DNA polymerase beta G231D crystallized in peg 400 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U8H
- Type
- protein + DNA
- Length
- 347 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
- NA
- Pockets
- 3 · best druggability 0.71
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 | 316 | 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*C)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, D, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.71 | 0.77 | 75 | empty |
| 2 | 172 | 0.61 | 0.84 | 23 | empty |
| 3 | 123 | 0.40 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- T–P · 479 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–T · 463 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 365 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 328 Ų buried · 6 hydrogen bonds · protein-nucleic
- T–D · 231 Ų buried · 21 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 5U8H · PDBe 5U8H · UniProt P06746
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