Research workbench
Structure of no-DNA factor
Analyse Structure of no-DNA factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GCL
- Type
- protein + DNA
- Length
- 1,580 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoid occlusion factor slma; DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3')
- UniProt
- Q1R4V1
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, H | Nucleoid occlusion factor slma | protein | 190 | 75% helix, 0% strand | Q1R4V1 |
| B | Nucleoid occlusion factor slma | protein | 196 | 75% helix, 0% strand | Q1R4V1 |
| D, F | Nucleoid occlusion factor slma | protein | 189 | 73% helix, 0% strand | Q1R4V1 |
| W, Z, R, T | DNA (5'-D(*AP*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*CP*T)-3') | dna | 14 | — | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.72 | 0.78 | 71 | empty |
| 2 | 205 | 0.68 | 0.86 | 37 | empty |
| 3 | 85 | 0.56 | 0.87 | 21 | empty |
| 4 | 376 | 0.56 | 0.75 | 36 | empty |
| 5 | 356 | 0.55 | 0.75 | 30 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1789 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1745 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1742 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1713 Ų buried · 32 hydrogen bonds · protein-protein
- R–T · 625 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 4GCL · structure of no-dna factor · 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 Q1R4V1
- Elsewhere: RCSB PDB 4GCL · PDBe 4GCL · UniProt Q1R4V1
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