Research workbench
Human APE1 phosphorothioate substrate complex with MN2+
Analyse Human APE1 phosphorothioate substrate complex with MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DG0
- Type
- protein + DNA
- Length
- 583 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, MN, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 30% 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 | 28% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 266 | 32% 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
- MN · Manganese (II) ion · metal · 7 copies · chains A, P, V, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.66 | 0.85 | 35 | 48Z, MN, EDO |
| 2 | 340 | 0.64 | 0.80 | 38 | empty |
| 3 | 238 | 0.52 | 0.76 | 40 | empty |
| 4 | 110 | 0.50 | 0.81 | 18 | empty |
| 5 | 197 | 0.47 | 0.75 | 19 | MN |
Interfaces
4 interfaces between chains.
- P–V · 918 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- A–B · 811 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 727 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–V · 600 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 5DG0 · Human APE1 phosphorothioate substrate complex with Mn2+ · 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 B against A, TM-score 1.00
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 5DG0 · PDBe 5DG0 · UniProt P27695
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