Research workbench
The crystal structure of the transcriptional regulator (gntr family) from enterococcus faecalis V583
Analyse The crystal structure of the transcriptional regulator (gntr family) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDV
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator (gntr family)
- Ligands
- MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator (gntr family) | protein | 121 | 13% helix, 53% strand | — |
| B | Transcriptional regulator (gntr family) | protein | 139 | 25% helix, 47% strand | — |
| C | Transcriptional regulator (gntr family) | protein | 120 | 14% helix, 54% strand | — |
| D | Transcriptional regulator (gntr family) | protein | 138 | 25% helix, 47% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.75 | 0.85 | 58 | empty |
| 2 | 564 | 0.71 | 0.79 | 52 | empty |
| 3 | 584 | 0.69 | 0.78 | 61 | empty |
| 4 | 96 | 0.35 | 0.74 | 16 | MG |
| 5 | 72 | 0.30 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1042 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 417 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 248 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3DDV · The crystal structure of the transcriptional regulator (GntR family) from Enterococcus… · 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
- Elsewhere: RCSB PDB 3DDV · PDBe 3DDV
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