MolNFT v1 · #88037 · protein + DNA
Structure of mutm in complex with carbocyclic 8-oxo-G containing DNA
4CIS · Formamidopyrimidin DNA glycosylase: “Structure of mutm in complex with carbocyclic 8-oxo-G containing DNA”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.82). MolNFT v1 #88037 on GenesisL1: 3D structure, binding…
- PDB
- 4CIS
- Type
- protein + DNA
- Length
- 558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidin DNA glycosylase; DNA
- EC
- 3.2.2.23
- UniProt
- Q031W6
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidopyrimidin DNA glycosylase (EC 3.2.2.23) | protein | 263 | 33% helix, 24% strand | Q031W6 |
| B | Formamidopyrimidin DNA glycosylase (EC 3.2.2.23) | protein | 267 | 33% helix, 24% strand | Q031W6 |
| C | DNA | dna | 14 | — | — |
| D | DNA | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.82 | 0.83 | 72 | empty |
| 2 | 488 | 0.68 | 0.79 | 48 | BU3 |
| 3 | 289 | 0.55 | 0.76 | 32 | empty |
| 4 | 94 | 0.41 | 0.78 | 14 | empty |
| 5 | 71 | 0.41 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–D · 796 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 567 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 537 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–D · 467 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 280 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4CIS · Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA · 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 Q031W6
- Elsewhere: RCSB PDB 4CIS · PDBe 4CIS · UniProt Q031W6
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