MolNFT v1 · #78123 · protein + DNA
Duplex interrogation by a direct DNA repair protein in the search of damage
3RZH · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2: “Duplex interrogation by a direct DNA repair protein in the search of damage”. X-ray diffraction, 1 ligand (XL3), 3 pockets (best druggability 0.74). MolNFT v1 #78123 on…
- PDB
- 3RZH
- Type
- protein + DNA
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2…
- EC
- 1.14.11.-
- UniProt
- Q6NS38
- Ligands
- XL3
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.-) | protein | 201 | 18% helix, 41% strand | Q6NS38 |
| B | 5'-D(*CP*TP*GP*TP*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3' | dna | 13 | — | — |
| C | 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3' | dna | 13 | — | — |
Ligands and binding sites
- XL3 · propane-1-thiol · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.74 | 0.81 | 44 | XL3 |
| 2 | 310 | 0.52 | 0.74 | 22 | empty |
| 3 | 69 | 0.42 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 704 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 507 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–C · 491 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 3RZH · Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage · the same entry in another collection · chain B against B, TM-score 1.00
- Q6NS38 · AlphaFold monomer V2.0 prediction for DNA oxidative demethylase ALKBH2 (Q6NS38) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q6NS38
- Elsewhere: RCSB PDB 3RZH · PDBe 3RZH · UniProt Q6NS38
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