MolNFT v1 · #144279 · protein + DNA
Human APE1 substrate complex with an G/G mismatch adjacent the thf
6BOR · DNA-(apurinic or apyrimidinic site) lyase: “Human APE1 substrate complex with an G/G mismatch adjacent the thf”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.66). MolNFT v1 #144279 on GenesisL1: 3D structure…
- PDB
- 6BOR
- Type
- protein + DNA
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-(apurinic or apyrimidinic site) lyase; 21-mer DNA
- EC
- 3.1.-.-, 4.2.99.18
- UniProt
- P27695
- Ligands
- CL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 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 | 29% helix, 24% strand | P27695 |
| B | DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-, 4.2.99.18) | protein | 266 | 30% helix, 25% strand | P27695 |
| P | 21-mer DNA | dna | 21 | — | — |
| V | 21-mer DNA | dna | 21 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.66 | 0.80 | 33 | empty |
| 2 | 251 | 0.54 | 0.77 | 30 | empty |
| 3 | 94 | 0.49 | 0.82 | 18 | empty |
| 4 | 170 | 0.47 | 0.76 | 26 | empty |
| 5 | 90 | 0.36 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- P–V · 910 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–P · 801 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 784 Ų buried · 11 hydrogen bonds · protein-protein
- A–V · 563 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BOR · Human APE1 substrate complex with an G/G mismatch adjacent the THF · the same entry in another collection · chain A against A, TM-score 1.00
- P27695 · AlphaFold monomer V2.0 prediction for DNA-(apurinic or apyrimidinic site) endonuclease… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 6BOR · PDBe 6BOR · UniProt P27695
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