MolNFT v1 · #156973 · protein
Crystallographic solvent mapping analysis of DMSO/TRIS bound to APE1
6MKM · DNA-(apurinic or apyrimidinic site) lyase: “Crystallographic solvent mapping analysis of DMSO/TRIS bound to APE1”. X-ray diffraction, 4 pockets (best druggability 0.37). MolNFT v1 #156973 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MKM
- Type
- protein
- Length
- 281 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
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 281 | 27% helix, 25% strand | P27695 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · 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 | 104 | 0.37 | 0.75 | 17 | TRS, DMS |
| 2 | 68 | 0.35 | 0.77 | 16 | DMS |
| 3 | 51 | 0.31 | 0.77 | 14 | empty |
| 4 | 59 | 0.30 | 0.75 | 16 | empty |
Compared structures
- 6MKM · Crystallographic solvent mapping analysis of DMSO/Tris 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 6MKM · PDBe 6MKM · UniProt P27695
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