MolNFT v1 · #167953 · protein + DNA
APE1 endonuclease product complex D148E
6W0Q · DNA-(apurinic or apyrimidinic site) lyase: “APE1 endonuclease product complex D148E”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.62). MolNFT v1 #167953 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6W0Q
- Type
- protein + DNA
- Length
- 584 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
- 10 · best druggability 0.62
Structure
x-ray diffraction · 5 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 |
| D | DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| 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
- MG · Magnesium ion · metal · chains A, D, P
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.62 | 0.80 | 32 | empty |
| 2 | 299 | 0.60 | 0.79 | 39 | empty |
| 3 | 229 | 0.52 | 0.76 | 33 | empty |
| 4 | 98 | 0.48 | 0.81 | 18 | empty |
| 5 | 111 | 0.40 | 0.76 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 812 Ų buried · 11 hydrogen bonds · protein-protein
- A–V · 588 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 573 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–V · 462 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- P–V · 457 Ų buried · 42 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 6W0Q · PDBe 6W0Q · UniProt P27695
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