MolNFT v1 · #68277 · protein + DNA
Mutm lesion recognition control complex with N174C crosslinking site
3JR5 · DNA glycosylase: “Mutm lesion recognition control complex with N174C crosslinking site”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.64). MolNFT v1 #68277 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3JR5
- Type
- protein + DNA
- Length
- 302 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA glycosylase; DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)- 3'); DNA…
- EC
- 4.2.99.18
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA glycosylase (EC 4.2.99.18) | protein | 273 | 30% helix, 24% strand | P84131 |
| B | DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(OGX) P*AP*GP*TP*CP*TP*AP*CP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
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 | 346 | 0.64 | 0.79 | 37 | GOL |
| 2 | 264 | 0.58 | 0.79 | 22 | empty |
| 3 | 178 | 0.47 | 0.76 | 27 | empty |
| 4 | 67 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 840 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 635 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 589 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3JR5 · MutM lesion recognition control complex with N174C crosslinking site · 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 P84131
- Elsewhere: RCSB PDB 3JR5 · PDBe 3JR5 · UniProt P84131
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