MolNFT v1 · #78525 · protein + DNA
Mutm slanted complex 7
3SBJ · Formamidopyrimidine-DNA glycosylase: “Mutm slanted complex 7”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.52). MolNFT v1 #78525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SBJ
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*G)-3'…
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidopyrimidine-DNA glycosylase | protein | 252 | 30% helix, 26% strand | P84131 |
| B | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*G)-3' | dna | 11 | — | — |
| C | 5'-D(P*CP*CP*TP*GP*GP*TP*(CX)P*TP*AP*CP*C)-3' | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.52 | 0.79 | 22 | empty |
| 2 | 103 | 0.46 | 0.80 | 19 | empty |
| 3 | 108 | 0.38 | 0.75 | 19 | empty |
| 4 | 90 | 0.37 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 627 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 514 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 495 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SBJ · MutM slanted complex 7 · 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 3SBJ · PDBe 3SBJ · UniProt P84131
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.