MolNFT v1 · #116496 · protein + DNA
Human APE1 mismatch product complex
5DFH · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 mismatch product complex”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.65). MolNFT v1 #116496 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DFH
- Type
- protein + DNA
- Length
- 581 residues
- Chains
- 5
- 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
- MG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 5 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 | 275 | 28% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 264 | 30% helix, 25% strand | P27695 |
| D | DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
| 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 | — | — |
| C | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
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 | 399 | 0.65 | 0.79 | 44 | empty |
| 2 | 238 | 0.58 | 0.79 | 32 | MG |
| 3 | 216 | 0.54 | 0.78 | 29 | empty |
| 4 | 116 | 0.52 | 0.81 | 18 | empty |
| 5 | 176 | 0.48 | 0.76 | 27 | empty |
Interfaces
7 interfaces between chains.
- A–B · 821 Ų buried · 13 hydrogen bonds · protein-protein
- A–V · 618 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 556 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–V · 470 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- V–C · 462 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (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 5DFH · PDBe 5DFH · UniProt P27695
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