MolNFT v1 · #12407 · protein + DNA
Crystal structure of lactococcus lactis formamido-pyrimidine DNA glycosylase (alias fpg or mutm) non covalently bound to an ap site containing DNA.
1KFV · 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3': “Crystal structure of lactococcus lactis formamido-pyrimidine DNA glycosylase (alias fpg or mutm) non…”. X-ray diffraction, 2 ligands (PDI, ZN), 7 pockets (best druggability…
- PDB
- 1KFV
- Type
- protein + DNA
- Length
- 574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- PDI, ZN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, G | 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3' | dna | 12 | — | — |
| E, H | 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3' | dna | 13 | — | — |
| A | Formamido-pyrimidine DNA glycosylase (EC 3.2.2.23) | protein | 264 | 33% helix, 25% strand | P42371 |
| B | Formamido-pyrimidine DNA glycosylase (EC 3.2.2.23) | protein | 260 | 34% helix, 25% strand | P42371 |
Ligands and binding sites
- PDI · Phosphoric acid mono-(3-hydroxy-propyl) ester · ligand · 2 copies · chains D, A, G, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains D, A, G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.68 | 0.79 | 38 | empty |
| 2 | 499 | 0.67 | 0.79 | 42 | empty |
| 3 | 514 | 0.66 | 0.77 | 47 | PDI |
| 4 | 257 | 0.54 | 0.76 | 26 | empty |
| 5 | 305 | 0.52 | 0.74 | 39 | PDI |
Interfaces
7 interfaces between chains.
- D–A · 628 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–B · 623 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–E · 528 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- G–H · 523 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–A · 362 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 1KFV · Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg… · the same entry in another collection · chain H against H, TM-score 1.00
- P42371 · AlphaFold monomer V2.0 prediction for formamidopyrimidine-DNA glycosylase (P42371) · a predicted model of the same protein · 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 P42371
- Elsewhere: RCSB PDB 1KFV · PDBe 1KFV · UniProt P42371
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