MolNFT v1 · #122710 · protein
Crystal structure of burkholderia cenocepacia bcna
5IXH · Ycei-like domain protein: “Crystal structure of burkholderia cenocepacia bcna”. X-ray diffraction, 2 ligands (OTP, SO4), 4 pockets (best druggability 0.85). MolNFT v1 #122710 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IXH
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycei-like domain protein
- UniProt
- U1XQX6
- Ligands
- OTP, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ycei-like domain protein | protein | 159 | 16% helix, 53% strand | U1XQX6 |
| B | Ycei-like domain protein | protein | 161 | 17% helix, 55% strand | U1XQX6 |
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 · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.85 | 0.92 | 60 | OTP |
| 2 | 419 | 0.85 | 0.92 | 57 | OTP |
| 3 | 272 | 0.56 | 0.77 | 32 | empty |
| 4 | 211 | 0.51 | 0.77 | 28 | SO4 |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5IXH · Crystal Structure of Burkholderia cenocepacia BcnA · 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 U1XQX6
- Elsewhere: RCSB PDB 5IXH · PDBe 5IXH · UniProt U1XQX6
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