Research workbench
The crystal structure of E. COLI muts binding to DNA with an unpaired thymidine
Analyse The crystal structure of E. COLI muts binding to DNA with an unpaired thymidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OH8
- Type
- protein + DNA
- Length
- 1,570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein muts; 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP…
- UniProt
- P23909
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein muts | protein | 788 | 46% helix, 19% strand | P23909 |
| B | DNA mismatch repair protein muts | protein | 754 | 47% helix, 17% strand | P23909 |
| E | 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP* TP*AP*T)-3' | dna | 14 | — | — |
| F | 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*CP*TP*TP*GP*GP*CP* AP*GP*CP*T)-3' | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.75 | 0.79 | 83 | empty |
| 2 | 489 | 0.69 | 0.80 | 66 | ADP, MG |
| 3 | 339 | 0.69 | 0.82 | 43 | empty |
| 4 | 231 | 0.66 | 0.85 | 29 | empty |
| 5 | 492 | 0.65 | 0.77 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2723 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 652 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 626 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–E · 542 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–E · 376 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1OH8 · The crystal structure of E. COLI muts binding to DNA with an unpaired thymidine · the same entry in another collection · chain A against A, TM-score 1.00
- P23909 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein muts (P23909) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P23909
- Elsewhere: RCSB PDB 1OH8 · PDBe 1OH8 · UniProt P23909
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