Research workbench
APE1 Y269A product complex with abasic DNA
Analyse APE1 Y269A product complex with abasic DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W4I
- Type
- protein + DNA
- Length
- 636 residues
- Chains
- 8
- 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
- MN
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 29% helix, 25% strand | P27695 |
| D, C | DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') | dna | 11 | — | — |
| P, E | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| V, F | DNA (5'- D(P*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
- MN · Manganese (II) ion · metal · 2 copies · chains A, D, P, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.60 | 0.74 | 61 | empty |
| 2 | 191 | 0.52 | 0.78 | 30 | empty |
| 3 | 177 | 0.48 | 0.77 | 21 | empty |
| 4 | 192 | 0.47 | 0.75 | 24 | empty |
| 5 | 68 | 0.38 | 0.79 | 12 | empty |
Interfaces
13 interfaces between chains.
- A–V · 597 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 582 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 544 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 508 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–V · 465 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 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 6W4I · PDBe 6W4I · UniProt P27695
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