MolNFT v1 · #78127 · protein + DNA
Duplex interrogation by a direct DNA repair protein in the search of damage
3RZL · 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), 9 pockets (best druggability 0.80). MolNFT v1 #78127 on…
- PDB
- 3RZL
- Type
- protein + DNA
- Length
- 445 residues
- Chains
- 6
- 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
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.-) | protein | 194 | 18% helix, 42% strand | Q6NS38 |
| B, E | 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3' | dna | 13 | — | — |
| C, F | 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3' | dna | 13 | — | — |
| D | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.-) | protein | 199 | 16% helix, 42% strand | Q6NS38 |
Ligands and binding sites
- XL3 · propane-1-thiol · ligand · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.80 | 0.82 | 96 | empty |
| 2 | 555 | 0.75 | 0.83 | 35 | XL3 |
| 3 | 66 | 0.74 | 0.99 | 21 | empty |
| 4 | 58 | 0.72 | 0.99 | 20 | empty |
| 5 | 524 | 0.71 | 0.80 | 38 | XL3 |
Interfaces
9 interfaces between chains.
- D–E · 659 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 638 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–F · 630 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 579 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–F · 560 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3RZL · Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage · the same entry in another collection · chain F against F, TM-score 1.00
- Q6NS38 · AlphaFold monomer V2.0 prediction for DNA oxidative demethylase ALKBH2 (Q6NS38) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 3RZL · PDBe 3RZL · UniProt Q6NS38
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