Research workbench
Structural genomics, protein ybgi, unknown function
Analyse Structural genomics, protein ybgi, unknown function in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NMO
- Type
- protein
- Length
- 1,482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ybgi
- UniProt
- P75743
- Ligands
- FE
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hypothetical protein ybgi | protein | 247 | 38% helix, 25% strand | P75743 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.78 | 0.80 | 95 | empty |
| 2 | 1074 | 0.75 | 0.78 | 92 | FE |
| 3 | 1029 | 0.75 | 0.78 | 94 | FE |
| 4 | 957 | 0.74 | 0.78 | 92 | FE |
| 5 | 562 | 0.71 | 0.79 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1155 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1111 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1098 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 434 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 335 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1NMO · Structural genomics, protein ybgI, unknown function · 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 P75743
- Elsewhere: RCSB PDB 1NMO · PDBe 1NMO · UniProt P75743
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