MolNFT v1 · #78501 · protein + DNA
Mutm slanted complex 8
3SAV · DNA glycosylase: “Mutm slanted complex 8”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.63). MolNFT v1 #78501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SAV
- Type
- protein + DNA
- Length
- 276 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*AP*AP*GP*GP*AP*CP*GP*C)- 3'); DNA…
- EC
- 4.2.99.18
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA glycosylase (EC 4.2.99.18) | protein | 252 | 30% helix, 25% strand | P84131 |
| C | DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*AP*AP*GP*GP*AP*CP*GP*C)- 3') | dna | 13 | — | — |
| D | DNA (5'-D(*TP*GP*CP*GP*T*CP*CP*TP*TP*GP*TP*(CX2) 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.63 | 0.80 | 43 | empty |
| 2 | 178 | 0.52 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 556 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–D · 532 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–C · 517 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SAV · MUTM Slanted complex 8 · 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 3SAV · PDBe 3SAV · UniProt P84131
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