MolNFT v1 · #61180 · protein
The crystal structure of the transcriptional regulator (gntr family) from enterococcus faecalis V583
3DDV: “The crystal structure of the transcriptional regulator (gntr family) from enterococcus faecalis V583”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.75). MolNFT v1 #61180 on GenesisL1: 3D structure, binding sites…
- 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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