Research workbench
Crystal structure of the ligand binding domain of lysr-type transcriptional regulator, occr from agrobacterium tumefaciens in the complex with octopine
Analyse Crystal structure of the ligand binding domain of lysr-type transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VVI
- Type
- protein
- Length
- 615 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octopine CATABOLISM/UPTAKE operon regulatory protein occr
- UniProt
- P0A4T4
- Ligands
- 6DB, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octopine CATABOLISM/UPTAKE operon regulatory protein occr | protein | 208 | 37% helix, 27% strand | P0A4T4 |
| B | Octopine CATABOLISM/UPTAKE operon regulatory protein occr | protein | 203 | 37% helix, 28% strand | P0A4T4 |
| C | Octopine CATABOLISM/UPTAKE operon regulatory protein occr | protein | 204 | 38% helix, 28% strand | P0A4T4 |
Ligands and binding sites
- 6DB · octopine · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- ACY · Acetic acid · additive · chains B, C
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 | 690 | 0.77 | 0.82 | 90 | 6DB, ACY |
| 2 | 380 | 0.64 | 0.79 | 62 | 6DB |
| 3 | 138 | 0.56 | 0.83 | 24 | empty |
| 4 | 96 | 0.48 | 0.81 | 26 | CL |
| 5 | 70 | 0.32 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1478 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 5VVI · Crystal Structure of the Ligand Binding Domain of LysR-type Transcriptional Regulator… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A4T4 · AlphaFold monomer V2.0 prediction for octopine CATABOLISM/UPTAKE operon regulatory… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0A4T4
- Elsewhere: RCSB PDB 5VVI · PDBe 5VVI · UniProt P0A4T4
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