MolNFT v1 · #67818 · protein
The structure of a possible transposon-related DNA-binding protein from clostridium difficile 630.
3IVP · Putative transposon-related DNA-binding protein: “The structure of a possible transposon-related DNA-binding protein from clostridium difficile 630.”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #67818 on…
- PDB
- 3IVP
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transposon-related DNA-binding protein
- UniProt
- Q180H4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transposon-related DNA-binding protein | protein | 115 | 65% helix, 0% strand | Q180H4 |
| B | Putative transposon-related DNA-binding protein | protein | 111 | 66% helix, 0% strand | Q180H4 |
| C | Putative transposon-related DNA-binding protein | protein | 111 | 67% helix, 0% strand | Q180H4 |
| D | Putative transposon-related DNA-binding protein | protein | 115 | 67% helix, 0% strand | Q180H4 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 3 copies · chains C, A, D
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 | 850 | 0.70 | 0.76 | 79 | PG4 |
| 2 | 104 | 0.42 | 0.77 | 20 | empty |
| 3 | 52 | 0.31 | 0.77 | 16 | empty |
| 4 | 64 | 0.30 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2369 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2345 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 421 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 158 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3IVP · The structure of a possible transposon-related DNA-binding protein from Clostridium… · 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 Q180H4
- Elsewhere: RCSB PDB 3IVP · PDBe 3IVP · UniProt Q180H4
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