MolNFT v1 · #162931 · protein + DNA
Crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor
6RNM · Formamidopyrimidine-DNA glycosylase: “Crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor”. X-ray diffraction, 2 ligands (KB5, ZN), 4 pockets (best druggability 0.71). MolNFT v1 #162931 on GenesisL1…
- PDB
- 6RNM
- Type
- protein + DNA
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- A0A165FVI1
- Ligands
- KB5, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 271 | 33% helix, 23% strand | A0A165FVI1 |
| D | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 14 | — | — |
| E | DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- KB5 · 6-azanyl-9~{H}-purine-8-thiol · ligand · chains A, D
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.71 | 0.78 | 44 | KB5 |
| 2 | 362 | 0.66 | 0.80 | 37 | empty |
| 3 | 132 | 0.43 | 0.76 | 19 | GOL |
| 4 | 58 | 0.31 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 709 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 544 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–E · 429 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6RNM · Crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor · 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 A0A165FVI1
- Elsewhere: RCSB PDB 6RNM · PDBe 6RNM · UniProt A0A165FVI1
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