Research workbench
Ycfi, a putative structural protein from rhodopseudomonas palustris.
Analyse Ycfi, a putative structural protein from rhodopseudomonas palustris. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GYQ
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycfi, putative structural protein
- Ligands
- ZN, FE, NA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ycfi, putative structural protein | protein | 162 | 78% helix, 1% strand | — |
| B | Ycfi, putative structural protein | protein | 157 | 81% helix, 1% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FE · Fe (III) ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.63 | 0.86 | 34 | ACT |
| 2 | 96 | 0.59 | 0.87 | 28 | empty |
| 3 | 107 | 0.39 | 0.76 | 22 | ACT |
| 4 | 96 | 0.39 | 0.76 | 20 | ACT |
| 5 | 83 | 0.35 | 0.75 | 18 | ZN |
Interfaces
1 interface between chains.
- A–B · 1749 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2GYQ · YcfI, a putative structural protein from Rhodopseudomonas palustris. · 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
- Elsewhere: RCSB PDB 2GYQ · PDBe 2GYQ
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