Research workbench
The crystal structure of E. COLI muts binding to DNA with a G:G mismatch
Analyse The crystal structure of E. COLI muts binding to DNA with a G:G mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OH7
- Type
- protein + DNA
- Length
- 1,577 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
- 17 · best druggability 0.78
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 | 45% 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 | 18 | — | — |
| F | 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*GP*TP*GP*GP *CP*AP*GP*CP*T)-3' | dna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.78 | 0.80 | 107 | empty |
| 2 | 819 | 0.77 | 0.81 | 76 | empty |
| 3 | 538 | 0.70 | 0.79 | 73 | ADP, MG |
| 4 | 282 | 0.68 | 0.84 | 29 | empty |
| 5 | 450 | 0.64 | 0.77 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2688 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 811 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–E · 661 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–F · 649 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 389 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1OH7 · The crystal structure of E. COLI muts binding to DNA with a G:G mismatch · 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 1OH7 · PDBe 1OH7 · UniProt P23909
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