MolNFT v1 · #111398 · protein + DNA
Crystal structure of D144N muty bound to its anti-substrate
4YPR · A/G-specific adenine glycosylase: “Crystal structure of D144N muty bound to its anti-substrate”. X-ray diffraction, 1 ligand (SF4), 11 pockets (best druggability 0.79). MolNFT v1 #111398 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YPR
- Type
- protein + DNA
- Length
- 747 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A/G-specific adenine glycosylase; DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- P83847
- Ligands
- SF4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A/G-specific adenine glycosylase (EC 3.2.2.-) | protein | 355 | 46% helix, 15% strand | P83847 |
| B | A/G-specific adenine glycosylase (EC 3.2.2.-) | protein | 350 | 48% helix, 13% strand | P83847 |
| C, E | DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3') | dna | 10 | — | — |
| D, F | DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.79 | 0.82 | 57 | empty |
| 2 | 841 | 0.76 | 0.80 | 58 | empty |
| 3 | 127 | 0.69 | 0.90 | 25 | empty |
| 4 | 50 | 0.68 | 0.97 | 17 | SF4 |
| 5 | 381 | 0.66 | 0.80 | 39 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1001 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–F · 956 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 942 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 888 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 439 Ų buried · 37 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 P83847
- Elsewhere: RCSB PDB 4YPR · PDBe 4YPR · UniProt P83847
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