Research workbench
[4FE-4S]-nsrr complexed to 23-bp HMPA1 operator fragment
Analyse [4FE-4S]-nsrr complexed to 23-bp HMPA1 operator fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B0C
- Type
- protein + DNA
- Length
- 334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor nsrr; DNA (5'…
- UniProt
- Q9L132
- Ligands
- SF4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hth-type transcriptional repressor nsrr | protein | 144 | 54% helix, 6% strand | Q9L132 |
| C | DNA (5'- D(P*AP*AP*CP*AP*CP*GP*AP*AP*TP*AP*TP*CP*AP*TP*CP*TP*AP*CP*CP*AP*AP*TP *T)-3') | dna | 23 | — | — |
| D | DNA (5'- D(P*AP*AP*TP*TP*GP*GP*TP*AP*GP*AP*TP*GP*AP*TP*AP*TP*TP*CP*GP*TP*GP*TP *T)-3') | dna | 23 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 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 | 0.79 | 0.83 | 74 | SF4 |
| 2 | 72 | 0.40 | 0.80 | 17 | empty |
| 3 | 114 | 0.36 | 0.74 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2120 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1004 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–D · 508 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 489 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 476 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7B0C · [4Fe-4S]-NsrR complexed to 23-bp HmpA1 operator fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q9L132 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor nsrr (Q9L132) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9L132
- Elsewhere: RCSB PDB 7B0C · PDBe 7B0C · UniProt Q9L132
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