MolNFT v1 · #167461 · protein
Crystal structure of transcriptional regulator from bacteriophage 186
6VLI · Regulatory protein cii: “Crystal structure of transcriptional regulator from bacteriophage 186”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #167461 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VLI
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein cii
- UniProt
- P21678
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein cii | protein | 154 | 61% helix, 1% strand | P21678 |
| B | Regulatory protein cii | protein | 151 | 62% helix, 1% strand | P21678 |
| C | Regulatory protein cii | protein | 144 | 60% helix, 1% strand | P21678 |
| D | Regulatory protein cii | protein | 145 | 62% helix, 1% strand | P21678 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A, D
- SIN · Succinic acid · additive · chains A, D
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 383 | 0.73 | 0.84 | 62 | ACT, SIN |
| 2 | 346 | 0.73 | 0.85 | 53 | empty |
| 3 | 95 | 0.40 | 0.77 | 18 | empty |
| 4 | 56 | 0.36 | 0.79 | 18 | empty |
| 5 | 83 | 0.36 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3137 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2923 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 488 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 420 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 266 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VLI · Crystal structure of transcriptional regulator from bacteriophage 186 · 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 P21678
- Elsewhere: RCSB PDB 6VLI · PDBe 6VLI · UniProt P21678
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