MolNFT v1 · #57326 · protein + DNA
Crystal structure of MVNEI1/THF complex
3A46 · Formamidopyrimidine-DNA glycosylase: “Crystal structure of MVNEI1/THF complex”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #57326 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A46
- Type
- protein + DNA
- Length
- 628 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; DNA
- EC
- 3.2.2.23
- UniProt
- Q5UQ00
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) | protein | 288 | 31% helix, 25% strand | Q5UQ00 |
| C, E | DNA | dna | 13 | — | — |
| D, F | DNA | dna | 13 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.71 | 0.75 | 74 | empty |
| 2 | 535 | 0.66 | 0.77 | 49 | empty |
| 3 | 335 | 0.59 | 0.77 | 26 | empty |
| 4 | 228 | 0.56 | 0.78 | 21 | GOL |
| 5 | 293 | 0.54 | 0.75 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–D · 716 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 713 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 576 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- C–D · 564 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- B–E · 540 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3A46 · Crystal structure of MvNei1/THF complex · the same entry in another collection · chain A 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 Q5UQ00
- Elsewhere: RCSB PDB 3A46 · PDBe 3A46 · UniProt Q5UQ00
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