Research workbench
Crystal structure of ybjn, a putative transcription regulator from E. COLI
Analyse Crystal structure of ybjn, a putative transcription regulator from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VU7
- Type
- protein
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ybjn protein
- UniProt
- B7LD46
- Ligands
- CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ybjn protein | protein | 141 | 38% helix, 26% strand | B7LD46 |
| B | Ybjn protein | protein | 142 | 38% helix, 27% strand | B7LD46 |
| C | Ybjn protein | protein | 144 | 38% helix, 25% strand | B7LD46 |
| D | Ybjn protein | protein | 135 | 36% helix, 28% strand | B7LD46 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.78 | 0.97 | 37 | empty |
| 2 | 79 | 0.74 | 0.97 | 30 | empty |
| 3 | 442 | 0.69 | 0.80 | 55 | empty |
| 4 | 134 | 0.47 | 0.77 | 17 | empty |
| 5 | 104 | 0.44 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1202 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1188 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 864 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6VU7 · Crystal structure of YbjN, a putative transcription regulator from E. coli · 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 B7LD46
- Elsewhere: RCSB PDB 6VU7 · PDBe 6VU7 · UniProt B7LD46
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