MolNFT v1 · #116497 · protein + DNA
Human APE1 phosphorothioate substrate complex
5DFI · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 phosphorothioate substrate complex”. X-ray diffraction, 2 ligands (48Z, CL), 7 pockets (best druggability 0.63). MolNFT v1 #116497 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DFI
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- 48Z, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 29% 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 | 276 | 29% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 265 | 30% helix, 25% strand | P27695 |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z) P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 20 | — | — |
| V | DNA (5'- D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- 48Z · 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose · ligand · chains A, P
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, P, V, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.63 | 0.79 | 32 | empty |
| 2 | 159 | 0.63 | 0.85 | 34 | 48Z, EDO |
| 3 | 224 | 0.49 | 0.75 | 26 | empty |
| 4 | 95 | 0.49 | 0.81 | 18 | empty |
| 5 | 164 | 0.47 | 0.76 | 26 | empty |
Interfaces
4 interfaces between chains.
- P–V · 919 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- A–B · 840 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 714 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–V · 620 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
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 P27695
- Elsewhere: RCSB PDB 5DFI · PDBe 5DFI · UniProt P27695
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