Research workbench
Crystal structure of VV2_1132, a lysr family transcriptional regulator
Analyse Crystal structure of VV2_1132, a lysr family transcriptional regulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9S
- Type
- protein
- Length
- 1,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VV2_1132
- Ligands
- BR
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VV2_1132 | protein | 277 | 44% helix, 24% strand | — |
| B | VV2_1132 | protein | 272 | 41% helix, 24% strand | — |
| C | VV2_1132 | protein | 291 | 48% helix, 23% strand | — |
| D | VV2_1132 | protein | 293 | 44% helix, 24% strand | — |
Ligands and binding sites
- BR · Bromide ion · ion · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.88 | 0.89 | 94 | BR |
| 2 | 1033 | 0.86 | 0.87 | 107 | BR |
| 3 | 521 | 0.79 | 0.85 | 72 | empty |
| 4 | 523 | 0.72 | 0.81 | 56 | empty |
| 5 | 97 | 0.66 | 0.90 | 22 | BR |
Interfaces
6 interfaces between chains.
- A–C · 1847 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1719 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1661 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1108 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 997 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5Y9S · Crystal structure of VV2_1132, a LysR family transcriptional regulator · 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 5Y9S · PDBe 5Y9S
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