Research workbench
Crystallographic solvent mapping analysis of DMSO/MG bound to APE1
Analyse Crystallographic solvent mapping analysis of DMSO/MG bound to APE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MKK
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- MG
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 282 | 28% helix, 24% strand | P27695 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.43 | 0.75 | 28 | MG, DMS |
| 2 | 69 | 0.37 | 0.78 | 16 | empty |
| 3 | 84 | 0.35 | 0.75 | 21 | empty |
| 4 | 51 | 0.32 | 0.77 | 13 | empty |
Compared structures
- 6MKK · Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1 · the same entry in another collection · chain A against A, TM-score 1.00
- P27695 · AlphaFold monomer V2.0 prediction for DNA-(apurinic or apyrimidinic site) endonuclease… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P27695
- Elsewhere: RCSB PDB 6MKK · PDBe 6MKK · UniProt P27695
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