MolNFT v1 · #81058 · protein + DNA
C.ESP1396I bound to its highest affinity operator site om
3UFD · Regulatory protein: “C.ESP1396I bound to its highest affinity operator site om”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.63). MolNFT v1 #81058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UFD
- Type
- protein + DNA
- Length
- 381 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein; DNA (5'- D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3…
- UniProt
- Q8GGH0
- Ligands
- CL
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Regulatory protein | protein | 76 | 75% helix, 1% strand | Q8GGH0 |
| B | Regulatory protein | protein | 77 | 74% helix, 1% strand | Q8GGH0 |
| C, G | DNA (5'- D(*AP*TP*GP*TP*AP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*GP*AP*CP*A)-3') | dna | 19 | — | — |
| D, H | DNA (5'- D(*TP*TP*GP*TP*CP*GP*AP*CP*TP*AP*TP*AP*GP*TP*CP*TP*AP*CP*A)-3') | dna | 19 | — | — |
| F | Regulatory protein | protein | 76 | 75% helix, 1% strand | Q8GGH0 |
Ligands and binding sites
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.63 | 0.77 | 28 | empty |
| 2 | 98 | 0.40 | 0.77 | 17 | empty |
| 3 | 57 | 0.39 | 0.82 | 19 | empty |
| 4 | 82 | 0.39 | 0.78 | 14 | empty |
| 5 | 85 | 0.38 | 0.77 | 15 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1029 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1022 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 848 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- C–D · 844 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–D · 410 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3UFD · C.Esp1396I bound to its highest affinity operator site OM · 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 Q8GGH0
- Elsewhere: RCSB PDB 3UFD · PDBe 3UFD · UniProt Q8GGH0
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