Research workbench
Heme sensor protein pefr from streptococcus agalactiae bound to operator DNA (28-mer)
Analyse Heme sensor protein pefr from streptococcus agalactiae bound to operator DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DVV
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth marr-type domain-containing protein; DNA (28-mer)
- UniProt
- Q8E4J9
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth marr-type domain-containing protein | protein | 139 | 66% helix, 9% strand | Q8E4J9 |
| B | Hth marr-type domain-containing protein | protein | 140 | 66% helix, 9% strand | Q8E4J9 |
| L | DNA (28-mer) | dna | 28 | — | — |
| M | DNA (28-mer) | dna | 28 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.81 | 0.85 | 50 | empty |
| 2 | 696 | 0.77 | 0.83 | 47 | empty |
| 3 | 143 | 0.40 | 0.74 | 20 | empty |
| 4 | 70 | 0.33 | 0.75 | 17 | empty |
| 5 | 89 | 0.33 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1928 Ų buried · 5 hydrogen bonds · protein-protein
- L–M · 1232 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–M · 714 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–L · 688 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–M · 633 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7DVV · Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer) · 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 Q8E4J9
- Elsewhere: RCSB PDB 7DVV · PDBe 7DVV · UniProt Q8E4J9
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