MolNFT v1 · #168040 · protein + DNA
APE1 exonuclease substrate complex wild-type
6W3L · Tcgacggatcc: “APE1 exonuclease substrate complex wild-type”. X-ray diffraction, 2 ligands (NA, CA), 9 pockets (best druggability 0.57). MolNFT v1 #168040 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6W3L
- Type
- protein + DNA
- Length
- 594 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tcgacggatcc; GCTGATGCG(C7R); Ggatccgtcgatcgcatcagc; DNA-(apurinic or apyrimidinic site)…
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- NA, CA
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tcgacggatcc | dna | 11 | — | — |
| D | GCTGATGCG(C7R) | dna | 10 | — | — |
| E | Ggatccgtcgatcgcatcagc | dna | 21 | — | — |
| A, B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 276 | 30% helix, 25% strand | P27695 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains E, A
- CA · Calcium ion · metal · chains D
- EDO · 1,2-ethanediol · additive · chains A
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 | 207 | 0.57 | 0.80 | 29 | empty |
| 2 | 77 | 0.53 | 0.86 | 18 | empty |
| 3 | 248 | 0.51 | 0.75 | 29 | empty |
| 4 | 191 | 0.48 | 0.76 | 39 | empty |
| 5 | 191 | 0.46 | 0.74 | 21 | empty |
Interfaces
7 interfaces between chains.
- E–B · 552 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 549 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–B · 538 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 477 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- D–E · 426 Ų buried · 45 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 6W3L · PDBe 6W3L · UniProt P27695
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