Research workbench
ATP bound muts
Analyse ATP bound muts in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7A
- Type
- protein + DNA
- Length
- 1,588 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
- ATP, MG
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein muts | protein | 791 | 46% helix, 19% strand | P23909 |
| B | DNA mismatch repair protein muts | protein | 762 | 48% helix, 18% 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*TP*TP*GP*GP*CP*AP*GP* CP*T)-3' | dna | 17 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.78 | 0.81 | 100 | empty |
| 2 | 1085 | 0.76 | 0.78 | 122 | ATP, MG |
| 3 | 291 | 0.70 | 0.85 | 29 | empty |
| 4 | 361 | 0.70 | 0.83 | 53 | empty |
| 5 | 494 | 0.68 | 0.79 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2748 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 813 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–F · 657 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–E · 656 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–E · 328 Ų buried · 3 hydrogen bonds · protein-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 P23909
- Elsewhere: RCSB PDB 1W7A · PDBe 1W7A · UniProt P23909
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