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Crystal structure of E.COLI formamidopyrimidine-DNA glycosylase (fpg) covalently trapped with DNA
Analyse Crystal structure of E.COLI formamidopyrimidine-DNA glycosylase (fpg)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K82
- Type
- protein + DNA
- Length
- 1,144 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'…
- EC
- 3.2.2.23
- UniProt
- P05523
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3' | dna | 13 | — | — |
| I, J, K, L | 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)- 3' | dna | 13 | — | — |
| A, B, C, D | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) | protein | 260 | 27% helix, 24% strand | P05523 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.78 | 0.80 | 67 | empty |
| 2 | 1026 | 0.78 | 0.80 | 70 | empty |
| 3 | 872 | 0.69 | 0.75 | 75 | empty |
| 4 | 888 | 0.67 | 0.74 | 76 | empty |
| 5 | 696 | 0.66 | 0.75 | 51 | empty |
Interfaces
27 interfaces between chains.
- I–A · 778 Ų buried · 20 hydrogen bonds · protein-nucleic
- L–D · 775 Ų buried · 19 hydrogen bonds · protein-nucleic
- J–B · 773 Ų buried · 20 hydrogen bonds · protein-nucleic
- K–C · 757 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–C · 634 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1K82 · Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped… · the same entry in another collection · chain D against D, 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 P05523
- Elsewhere: RCSB PDB 1K82 · PDBe 1K82 · UniProt P05523
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