MolNFT v1 · #115483 · protein + DNA
Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site and a free nucleobase (100% product at 240 hours)
5CL9: “Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site and a free nucleobase (100% product…”. X-ray diffraction, 2 ligands (ORP, 54K), 1 pocket (best druggability 0.80). MolNFT v1 #115483 on GenesisL1: 3D structure…
- PDB
- 5CL9
- Type
- protein + DNA
- Length
- 254 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*(ORP)P*AP*GP*TP*CP*CP*G)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- R8GWR7
- Ligands
- ORP, 54K
- Pockets
- 1 · best druggability 0.80
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*(ORP)P*AP*GP*TP*CP*CP*G)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, B
- 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.80 | 0.82 | 63 | ORP, 54K |
Interfaces
3 interfaces between chains.
- B–C · 537 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–B · 437 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 309 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5CL9 · Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free… · 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 5CL9 · PDBe 5CL9 · UniProt R8GWR7
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