MolNFT v1 · #115478 · protein + DNA
Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine analog or DNA containing an abasic site and a free nucleobase (71% SUBSTRATE/29% product at 24 hours)
5CL4: “Alkylpurine DNA glycosylase alkd bound to DNA containing a 3- methyladenine analog or DNA containing an…”. X-ray diffraction, 1 ligand (54K), 2 pockets (best druggability 0.77). MolNFT v1 #115478 on GenesisL1: 3D structure, binding…
- PDB
- 5CL4
- Type
- protein + DNA
- Length
- 255 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkd; DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- R8GWR7
- Ligands
- 54K
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkd (EC 3.2.2.-) | protein | 231 | 71% helix, 1% strand | R8GWR7 |
| B | DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- 54K · 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.77 | 0.81 | 52 | empty |
| 2 | 345 | 0.58 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 554 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–B · 518 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 282 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 5CL4 · Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA… · 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 R8GWR7
- Elsewhere: RCSB PDB 5CL4 · PDBe 5CL4 · UniProt R8GWR7
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