MolNFT v1 · #116494 · protein + DNA
Human APE1 product complex
5DFF · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 product complex”. X-ray diffraction, 2 ligands (MG, CL), 9 pockets (best druggability 0.68). MolNFT v1 #116494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DFF
- Type
- protein + DNA
- Length
- 585 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; DNA…
- EC
- 4.2.99.18
- UniProt
- P27695
- Ligands
- MG, CL
- Pockets
- 9 · best druggability 0.68
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 4.2.99.18) | protein | 276 | 29% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) | protein | 267 | 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 | — | — |
| 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
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.68 | 0.80 | 40 | PEG |
| 2 | 259 | 0.59 | 0.79 | 33 | empty |
| 3 | 219 | 0.55 | 0.78 | 31 | empty |
| 4 | 182 | 0.48 | 0.76 | 26 | empty |
| 5 | 120 | 0.41 | 0.76 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 760 Ų buried · 12 hydrogen bonds · protein-protein
- A–V · 630 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 561 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–V · 464 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- P–V · 453 Ų buried · 39 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 5DFF · PDBe 5DFF · UniProt P27695
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