Research workbench
Crystal structure of YCF54 protein from thermosynechococcus elongatus, northeast structural genomics consortium target TER59
Analyse Crystal structure of YCF54 protein from thermosynechococcus elongatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZE
- Type
- protein
- Length
- 643 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YCF54 protein
- UniProt
- Q8DIT2
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | YCF54 protein | protein | 107 | 39% helix, 25% strand | Q8DIT2 |
| E | YCF54 protein | protein | 108 | 40% helix, 25% strand | Q8DIT2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.80 | 0.84 | 55 | PO4 |
| 2 | 478 | 0.79 | 0.87 | 49 | empty |
| 3 | 467 | 0.72 | 0.81 | 38 | empty |
| 4 | 107 | 0.68 | 0.91 | 26 | empty |
| 5 | 121 | 0.45 | 0.77 | 18 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1314 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 636 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 617 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 530 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3HZE · Crystal Structure of Ycf54 protein from Thermosynechococcus elongatus, Northeast… · 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 Q8DIT2
- Elsewhere: RCSB PDB 3HZE · PDBe 3HZE · UniProt Q8DIT2
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