Research workbench
Crystal structure of burkholderia cenocepacia bcnb
Analyse Crystal structure of burkholderia cenocepacia bcnb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXG
- Type
- protein
- Length
- 675 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycei
- UniProt
- A2VST2
- Ligands
- OTP
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D | Ycei | protein | 169 | 12% helix, 60% strand | A2VST2 |
| A | Ycei | protein | 168 | 13% helix, 60% strand | A2VST2 |
Ligands and binding sites
- OTP · (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl trihydrogen diphosphate · ligand · 4 copies · chains B, A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.86 | 0.92 | 60 | OTP |
| 2 | 528 | 0.85 | 0.90 | 65 | OTP |
| 3 | 531 | 0.85 | 0.90 | 67 | OTP |
| 4 | 591 | 0.85 | 0.89 | 75 | OTP |
| 5 | 524 | 0.71 | 0.80 | 60 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1451 Ų buried · 32 hydrogen bonds · protein-protein
- B–A · 1368 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 346 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5IXG · Crystal Structure of Burkholderia cenocepacia BcnB · the same entry in another collection · chain B against B, 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 A2VST2
- Elsewhere: RCSB PDB 5IXG · PDBe 5IXG · UniProt A2VST2
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